OmicSelector: Basic Functionality Tutorial.

Konrad Stawiski1* and Marcin Kaszkowiak1

1Department of Biostatistics and Translational Research, Medical University of Lodz, Lodz, Poland (https://biostat.umed.pl)

*konrad@konsta.com.pl

Package

OmicSelector 0.1.0

Contents

1 Introduction

…

2 Setup script

The package OmicSelector has a lot of requirements that are nessesary to run all the experiments. The script below will allow to install most of them. It is highly recommended to install those packages using the code below.

If you are using our docker enviorment to learn this package you should not run this again. It would be a waste of time. [However, if you wish, you can play with the code in the notebook. Click here.](If you are using our enviorment to learn this package you can tweak this code in the interactive notebook. Click here.

Setup script:

readLines("setup.R") %>% paste0(collapse = "\n") %>% cat
#> install.packages(c("remotes","devtools"),repos = "http://cran.r-project.org")
#> install.packages(c("rlang","ps"), type = "source")
#> install.packages(c("roxygen2", "plotly", "rJava", "mice", "MatchIt", "kableExtra"))
#> install.packages("BiocManager",repos = "http://cran.r-project.org")
#> install.packages("plotly")
#> install.packages("reticulate")
#> library(BiocManager)
#> BiocManager::install(c("remotes","plyr","dplyr","edgeR","epiDisplay","rsq","MASS","Biocomb","caret","dplyr",
#>                        "pROC","ggplot2","DMwR", "doParallel", "Boruta", "spFSR", "varSelRF", "stringr", "psych", "C50", "randomForest",
#>                        "foreach","data.table", "ROSE", "deepnet", "gridExtra", "stargazer","gplots","My.stepwise","snow", "sva", "Biobase",
#>                        "calibrate", "ggrepel", "networkD3", "VennDiagram","RSNNS", "kernlab", "car", "PairedData",
#>                        "profileR","classInt","kernlab","xgboost", "keras", "tidyverse", "cutpointr","tibble","tidyr", "rpart", "party", "mgcv", "GDCRNATools",
#>                        "imputeMissings", "visdat", "naniar", "stringr", "doParallel", "R.utils", "TCGAbiolinks", "GDCRNATools", "kableExtra", "VIM", "mice", "MatchIt", "XML", "rmarkdown", "xtable", "ComplexHeatmap","circlize","BiocStyle","magick"))
#> remotes::install_github("STATWORX/bounceR", force = T)
#> #remotes::install_github("rstudio/reticulate")
#> remotes::install_github("Thie1e/cutpointr", force = T)
#> remotes::install_github("vqv/ggbiplot", force = T)
#> library(keras)
#> install_keras(method = "conda") # must have anaconda installed first, if not just use: install_keras()
#> 
#> 
#> install_github("kstawiski/OmicSelector") # Install our package.

This code does not cover the installation of mxnet, which can be used for benchmarking of the selected miRNA sets. The mxnet is however built and installed in our docker enviorment.

You can run this code directly from GitHub:

library(devtools)
source_url("https://raw.githubusercontent.com/kstawiski/OmicSelector/master/vignettes/setup.R")

As the OmicSelector package is installed we can load it easly.

library(OmicSelector)

3 Getting the data

To present the package functionality, we will use the pan-cancer data from TCGA (https://portal.gdc.cancer.gov/repository). These two commands below will download and store all the necessary data in your working directory. Please note, that this process may take some time (depending on your network connection), but has to be performed only once.

OmicSelector_download_tissue_miRNA_data_from_TCGA()
OmicSelector_process_tissue_miRNA_TCGA(remove_miRNAs_with_null_var = T)

Both of those function produce 2 files: tissue_miRNA_counts.csv and tissue_miRNA_logtpm.csv. First of those files contains metadata and raw counts as declared in TCGA. The second is are log-transformed transcripts-per-million (TPM) counts. Let’s load counts files and see its summary.

suppressWarnings(suppressMessages(library(data.table)))
suppressWarnings(suppressMessages(library(knitr)))
orginal_TCGA_data = fread("tissue_miRNA_counts.csv.gz")
orginal_TCGA_data[orginal_TCGA_data == ""] = NA
OmicSelector_table(table(orginal_TCGA_data$primary_site, orginal_TCGA_data$sample_type))

	PrimaryTumor	SolidTissueNormal
Adrenal gland	80	0
Bladder	409	19
Brain	512	5
Breast	1078	104
Bronchus and lung	991	91
Cervix uteri	307	3
Corpus uteri|Stomach|Other and unspecified parts of tongue|Meninges|Other and unspecified male genital organs|Colon|Connective, subcutaneous and other soft tissues|Bones, joints and articular cartilage of limbs|Ovary|Retroperitoneum and peritoneum|Peripheral nerves and autonomic nervous system|Uterus, NOS|Kidney	259	0
Corpus uteri|Uterus, NOS	538	33
Esophagus|Stomach	184	13
Eye and adnexa	80	0
Heart, mediastinum, and pleura|Bronchus and lung	87	0
Heart, mediastinum, and pleura|Other endocrine glands and related structures|Adrenal gland|Connective, subcutaneous and other soft tissues|Other and ill-defined sites|Spinal cord, cranial nerves, and other parts of central nervous system|Retroperitoneum and peritoneum	179	3
Heart, mediastinum, and pleura|Testis|Stomach|Lymph nodes|Bones, joints and articular cartilage of other and unspecified sites|Brain|Thyroid gland|Small intestine|Colon|Connective, subcutaneous and other soft tissues|Other and unspecified major salivary glands|Retroperitoneum and peritoneum|Hematopoietic and reticuloendothelial systems|Breast	47	0
Heart, mediastinum, and pleura|Thymus	124	2
Kidney	873	130
Liver and intrahepatic bile ducts	372	50
Other and ill-defined sites in lip, oral cavity and pharynx|Palate|Other and unspecified parts of tongue|Hypopharynx|Tonsil|Oropharynx|Larynx|Other and unspecified parts of mouth|Gum|Floor of mouth|Bones, joints and articular cartilage of other and unspecified sites|Lip|Base of tongue	523	44
Other and unspecified parts of biliary tract|Gallbladder|Liver and intrahepatic bile ducts	36	9
Ovary	489	0
Pancreas	178	4
Prostate gland	494	52
Rectosigmoid junction|Colon	444	8
Rectosigmoid junction|Unknown|Rectum|Colon|Connective, subcutaneous and other soft tissues	161	3
Skin	97	2
Stomach	436	41
Testis	150	0
Thyroid gland	506	59
Uterus, NOS	57	0

Let’s consider a following exemplary problem..

We want to find the set of miRNAs the most specific to pancreatic cancer. We see that there are 178 cases of pancreatic cancer miRNA-seq results and only 4 solid tissue normal cases. However, we have multiple normal tissue miRNA-seq results from other projects that could be incorporated in the analysis. Let’s filter and label the samples of interest.

suppressWarnings(suppressMessages(library(dplyr)))

cancer_cases = filter(orginal_TCGA_data, primary_site == "Pancreas" & sample_type == "PrimaryTumor")
control_cases = filter(orginal_TCGA_data, sample_type == "SolidTissueNormal")

The pipeline requires the variable Class with two levels (Cancer and Control) to be present in the dataset.

cancer_cases$Class = "Cancer"
control_cases$Class = "Control"

dataset = rbind(cancer_cases, control_cases)

OmicSelector_table(table(dataset$Class), col.names = c("Class", "Number of cases"))

Class	Number of cases
Cancer	178
Control	675

boxplot(dataset$age_at_diagnosis ~ dataset$Class)

t.test(dataset$age_at_diagnosis ~ dataset$Class)
#> 
#>  Welch Two Sample t-test
#> 
#> data:  dataset$age_at_diagnosis by dataset$Class
#> t = 3.88, df = 360.55, p-value = 0.0001242
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>   693.0905 2117.7294
#> sample estimates:
#>  mean in group Cancer mean in group Control 
#>              23782.23              22376.82
OmicSelector_table(table(dataset$gender.x, dataset$Class))

	Cancer	Control
female	80	334
male	98	325

chisq.test(dataset$gender.x, dataset$Class)
#> 
#>  Pearson's Chi-squared test with Yates' continuity correction
#> 
#> data:  dataset$gender.x and dataset$Class
#> X-squared = 1.6241, df = 1, p-value = 0.2025

There is a stistically significant difference in age between classess. The gender was not associated with class. In order to increase feature selection performance, we will try to balance the sets by performing propensity score matching.

old_dataset = dataset  # backup
dataset = dataset[grepl("Adenocarcinomas", dataset$disease_type), ]
match_by = c("age_at_diagnosis", "gender.x")
tempdane = dplyr::select(dataset, match_by)
tempdane$Class = ifelse(dataset$Class == "Cancer", TRUE, FALSE)
suppressMessages(library(mice))
suppressMessages(library(MatchIt))
temp1 = mice(tempdane, m = 1)
#> 
#>  iter imp variable
#>   1   1  age_at_diagnosis
#>   2   1  age_at_diagnosis
#>   3   1  age_at_diagnosis
#>   4   1  age_at_diagnosis
#>   5   1  age_at_diagnosis
temp2 = temp1$data
temp3 = mice::complete(temp1)
temp3 = temp3[complete.cases(temp3), ]
tempform = OmicSelector_create_formula(match_by)
mod_match <- matchit(tempform, data = temp3)
newdata = match.data(mod_match)
dataset = dataset[as.numeric(rownames(newdata)), ]

Let’s check if there is any imbalance in the new, transformed dataset.

boxplot(dataset$age_at_diagnosis ~ dataset$Class)

t.test(dataset$age_at_diagnosis ~ dataset$Class)
#> 
#>  Welch Two Sample t-test
#> 
#> data:  dataset$age_at_diagnosis by dataset$Class
#> t = 0.090876, df = 351.63, p-value = 0.9276
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>  -827.5374  907.7172
#> sample estimates:
#>  mean in group Cancer mean in group Control 
#>              23782.23              23742.14
OmicSelector_table(table(dataset$gender.x, dataset$Class))

	Cancer	Control
female	80	79
male	98	99

chisq.test(dataset$gender.x, dataset$Class)
#> 
#>  Pearson's Chi-squared test with Yates' continuity correction
#> 
#> data:  dataset$gender.x and dataset$Class
#> X-squared = 0, df = 1, p-value = 1
fwrite(dataset, "balanced_dataset.csv.gz")

There are no significant differences in age or gender composition between classes now. We can proceed to standard filtering, log-transormation and TPM-normalization.

However, first, in order to stay consistent between different datasets, we need to standardise microRNA names. OmicSelector_correct_miRNA_names() unify the miRNA names between different versions of miRbase.

dataset = OmicSelector_correct_miRNA_names(dataset)  # Correct miRNA names based on the aliases. Useful when analyzing old datasets - to keep the results coherent with current knowledge.
danex = dplyr::select(dataset, starts_with("hsa"))  # Create data.frame or matrix with miRNA counts with miRNAs in columns and cases in rows.
metadane = dplyr::select(dataset, -starts_with("hsa"))  # Metadata with 'Class' variables.
OmicSelector_table(table(metadane$Class))  # Let's be sure that 'Class' variable is correct and contains only 'Cancer' and 'Control' cases.

Var1	Freq
Cancer	178
Control	178

ttpm = OmicSelector_counts_to_log10tpm(danex, metadane, ids = metadane$sample, filtr = T, filtr_minimalcounts = 100, filtr_howmany = 1/3)  # We will leave only the miRNAs which apeared with at least 100 counts in 1/3 of cases.
#> 
#> DGEList unfiltered object with TPM was saved as TPM_DGEList.rds.
#> DGEList filtered object with TPM was saved as TPM_DGEList_filtered.rds.
#> (After filtering) miRNAs left: 166 | filtered out: 2418.
#> Returned data are log10(TPM).

You might have noticed, that we have filtered out microRNAs not having at least 100 counts in 1/3 of samples. It was done to ensure that microRNAs selected as features for classifier (possibly used in clinic) would be detectable in other, cheaper methods, such as qPCR. After filtering there are 166 miRNAs left.

In the next step we will devide the dataset into training, testing and validation datasets. We strongly belive that hold-out validation is the most redundant validation method and although OmicSelector supports cross-validation, the hold-out validation is set by default in most cases. Thus, the rest of the analysis is dependent on existance of 3 seperate datasets:

• Training dataset (mixed_train.csv): By default 60%, used for differential expression, feature selection and model training.
• Testing dataset (mixed_test.csv): By default 20%, used for hyperparameter selection (in holdout=T mode)and for performance assessment.
• Validation dataset (mixed_valid.csv): By default 20%, used only for performance assessment.

The best signiture (best set of miRNAs for diagnostic test) can be selected based on all 3 datasets, 2 datasets or only validation set. The process of best signiture selection will be discussed below.

The split can be prepared manually by user (the pipeline expects to find mixed_*.csv files in working directory) or in a convinient way using OmicSelector_prepare_split(). Let’s do it now.

mixed = OmicSelector_prepare_split(metadane = metadane, ttpm = ttpm, train_proc = 0.6)
#> 
#> Saved 3 sets as csv in working directory. Retruned mixed dataset.

Let’s see a split summary.

mixed = fread("mixed.csv")
OmicSelector_table(table(mixed$Class, mixed$mix))

	test	train	valid
Cancer	36	107	35
Control	36	107	35

OmicSelector_table(cbind(mixed[1:10, c(100:105)], Class = mixed[1:10, "Class"]))

hsa-miR-30c-5p	hsa-miR-30c-2-3p	hsa-miR-30d-5p	hsa-miR-139-5p	hsa-miR-10a-5p	hsa-miR-10b-5p	Class.Class
2.598949	1.514444	3.802908	1.555401	4.735516	4.298381	Cancer
2.391663	1.416540	3.656058	1.326116	4.615369	3.946954	Cancer
2.576255	1.566166	3.721311	1.220338	4.385001	3.998914	Cancer
2.260492	1.401010	3.539243	1.924365	3.945605	4.486228	Cancer
2.595315	1.562735	3.571441	1.721510	4.519249	4.126032	Cancer
2.632860	1.723000	3.708020	2.120359	4.875796	3.887056	Cancer
2.747742	2.016887	3.852090	1.533525	3.961177	3.642831	Cancer
3.037578	1.880192	3.960987	1.798007	4.675070	4.133894	Cancer
2.598933	1.291485	3.581714	1.413095	4.580566	3.960672	Cancer
2.829601	1.494520	3.589292	1.755581	4.687104	4.209582	Cancer

We can see that the dataset was devided in balanced way. Now we are ready to move to the analysis…

4 Basic exploratory analysis

In biomarker studies we relay on validation. We perform hold-out validation, so the signature selection has to be based on training dataset only. Including testing and validation dataset in the exploratory analysis could lead to bias (‘data leakage’). In the following section we show how to use our package to perform quick exploratory analysis of miRNA-seq data.

dane = OmicSelector_load_datamix(use_smote_not_rose = T)  # load mixed_*.csv files
train = dane[[1]]
test = dane[[2]]
valid = dane[[3]]
train_smoted = dane[[4]]
trainx = dane[[5]]
trainx_smoted = dane[[6]]  # get the objects from list to make the code more readable.

ks_load_datamix() function loads the data created in preparation phase. It requires the output constructed by OmicSelector_prepare_split() function to be placed in working directory (‘wd’), thus files ‘mixed_train.csv’, ‘mixed_test.csv’ and ‘mixed_valid.csv’ have to exist in the directory. If you have split the data manually, there may be some imbalance of classes in train, test or validation datasets. If so, OmicSelector_prepare_split() perform balancing using:

1. ROSE (default): https://journal.r-project.org/archive/2014/RJ-2014-008/RJ-2014-008.pdf - by default we generate 10 * number of cases in orginal dataset.
2. SMOTE: https://arxiv.org/abs/1106.1813 - by defult we use ‘perc.under=100’ and ‘k=10’.

At the beging of the analysis we usually perform principal component analysis (PCA) to assess for any batch effect, possible outliers and get a general understanding of miRNA profile. The package can construct 2-dimentional biplot and 3-dimentional interactive scatterplot based on the computed components.

pca = OmicSelector_PCA(trainx, train$Class)
pca

3D PCA plot may not be shown correctly in Jupyter notebook, but you can check in e.g. R Studio that it worOmicSelector_

pca3d = OmicSelector_PCA_3D(trainx, train$Class)
pca3d

Now we can also correct the batch effect, if there is any. For example, you can use OmicSelector_combat() to do so. However, detailed demonstration is out of scope of this tutorial.

Usually, the next step in the exploratory analysis is to perform the differential expression analysis. Differential expression in our package is biomarker-discovery oriented, thus it uses t-test with the correction for multiple comparisons. The following table shows signifiantly differently expressed miRNAs after Benjamini-Hochberg correction.

de = OmicSelector_differential_expression_ttest(trainx, train$Class)
sig_de = de %>% dplyr::filter(`p-value BH` <= 0.05) %>% dplyr::arrange(`p-value BH`)  # leave only significant after Benjamini-Hochberg procedure and sort by ascending p-value
OmicSelector_table(sig_de)

miR	mean logtpm	median logtpm	SD logtpm	cancer mean	cancer median	cancer SD	control mean	control median	control SD	log10FC (subtr estim)	log10FC	log2FC	reversed_log10FC	reverse_log2FC	p-value	p-value Bonferroni	p-value Holm	-log10(p-value Bonferroni)	p-value BH
hsa.miR.21.5p	5.081371	5.120977	0.5409456	5.473043	5.559281	0.3042087	4.689698	4.744446	0.4309906	-0.7833450	0.7833450	2.6022157	0.7833450	2.6022157	0.0000000	0.0000000	0.0000000	32.2312221	0.0000000
hsa.miR.30e.3p	3.654915	3.620465	0.2922656	3.445100	3.469065	0.1835853	3.864731	3.891680	0.2215066	0.4196304	-0.4196304	-1.3939819	-0.4196304	-1.3939819	0.0000000	0.0000000	0.0000000	32.1422635	0.0000000
hsa.miR.30a.3p	3.861758	3.760500	0.5107622	3.494206	3.528067	0.2957390	4.229311	4.315264	0.4049904	0.7351047	-0.7351047	-2.4419651	-0.7351047	-2.4419651	0.0000000	0.0000000	0.0000000	31.8224321	0.0000000
hsa.miR.30c.2.3p	1.791478	1.685323	0.4609305	1.478041	1.473434	0.2548946	2.104915	2.062559	0.4044845	0.6268741	-0.6268741	-2.0824306	-0.6268741	-2.0824306	0.0000000	0.0000000	0.0000000	26.3237118	0.0000000
hsa.miR.132.3p	2.062941	2.061854	0.3206914	2.268277	2.222890	0.2453178	1.857606	1.842071	0.2476985	-0.4106709	0.4106709	1.3642193	0.4106709	1.3642193	0.0000000	0.0000000	0.0000000	23.2892084	0.0000000
hsa.miR.375.3p	3.851381	4.088129	1.1312626	4.572062	4.593208	0.6167635	3.130699	3.420583	1.0689350	-1.4413633	1.4413633	4.7881053	1.4413633	4.7881053	0.0000000	0.0000000	0.0000000	21.6930447	0.0000000
hsa.miR.217.5p	2.065790	1.932856	1.2184284	2.817892	2.596188	1.0079357	1.313689	1.247738	0.9084168	-1.5042026	1.5042026	4.9968529	1.5042026	4.9968529	0.0000000	0.0000000	0.0000000	21.0021448	0.0000000
hsa.miR.139.5p	1.916157	1.919751	0.4638487	1.634747	1.558070	0.3573670	2.197567	2.204857	0.3804627	0.5628209	-0.5628209	-1.8696506	-0.5628209	-1.8696506	0.0000000	0.0000000	0.0000000	20.0671420	0.0000000
hsa.miR.199a.5p	3.034892	3.117770	0.3929526	3.267832	3.318017	0.2924584	2.801951	2.808411	0.3394148	-0.4658802	0.4658802	1.5476204	0.4658802	1.5476204	0.0000000	0.0000000	0.0000000	18.7831163	0.0000000
hsa.miR.338.3p	2.743796	2.778247	0.4190933	2.991348	2.994550	0.3219668	2.496243	2.539407	0.3543332	-0.4951049	0.4951049	1.6447027	0.4951049	1.6447027	0.0000000	0.0000000	0.0000000	18.6530266	0.0000000
hsa.miR.199b.5p	2.146095	2.358829	0.6145137	2.504540	2.573683	0.3567535	1.787650	1.799962	0.6100440	-0.7168901	0.7168901	2.3814574	0.7168901	2.3814574	0.0000000	0.0000000	0.0000000	17.2507100	0.0000000
hsa.miR.127.5p	2.214220	2.327709	0.4803146	2.486170	2.478848	0.3020641	1.942270	1.939357	0.4722596	-0.5438996	0.5438996	1.8067954	0.5438996	1.8067954	0.0000000	0.0000000	0.0000000	16.1634770	0.0000000
hsa.miR.381.3p	1.720930	1.791253	0.4579339	1.974984	1.949285	0.3353016	1.466877	1.476716	0.4226746	-0.5081072	0.5081072	1.6878957	0.5081072	1.6878957	0.0000000	0.0000000	0.0000000	15.6751972	0.0000000
hsa.miR.127.3p	2.789656	2.829601	0.3874414	2.995898	3.006282	0.3147991	2.583413	2.568116	0.3415622	-0.4124850	0.4124850	1.3702456	0.4124850	1.3702456	0.0000000	0.0000000	0.0000000	14.1819049	0.0000000
hsa.miR.199a.3p	3.431280	3.533249	0.3595668	3.620030	3.670480	0.2685999	3.242530	3.285480	0.3401837	-0.3775004	0.3775004	1.2540293	0.3775004	1.2540293	0.0000000	0.0000000	0.0000000	13.5707699	0.0000000
hsa.miR.181b.5p	2.447025	2.523360	0.4131408	2.664941	2.705753	0.2848923	2.229109	2.205351	0.4073655	-0.4358316	0.4358316	1.4478013	0.4358316	1.4478013	0.0000000	0.0000000	0.0000000	13.5990480	0.0000000
hsa.miR.199b.3p	3.430095	3.531945	0.3598114	3.619075	3.669630	0.2686093	3.241115	3.284615	0.3404382	-0.3779599	0.3779599	1.2555557	0.3779599	1.2555557	0.0000000	0.0000000	0.0000000	13.5889555	0.0000000
hsa.miR.194.5p	3.119571	3.359054	0.8329947	3.562675	3.633752	0.4167141	2.676468	2.410622	0.9078933	-0.8862067	0.8862067	2.9439150	0.8862067	2.9439150	0.0000000	0.0000000	0.0000000	13.2390851	0.0000000
hsa.miR.134.5p	2.366486	2.433393	0.4088244	2.572458	2.557931	0.2993653	2.160514	2.115254	0.4007277	-0.4119434	0.4119434	1.3684465	0.4119434	1.3684465	0.0000000	0.0000000	0.0000000	12.1552043	0.0000000
hsa.miR.30a.5p	4.429837	4.356060	0.4519742	4.199892	4.226049	0.2683567	4.659782	4.685628	0.4813796	0.4598896	-0.4598896	-1.5277200	-0.4598896	-1.5277200	0.0000000	0.0000000	0.0000000	12.1052493	0.0000000
hsa.miR.200a.5p	2.480123	2.527551	0.5262405	2.744628	2.777438	0.3622178	2.215619	2.330898	0.5329388	-0.5290086	0.5290086	1.7573286	0.5290086	1.7573286	0.0000000	0.0000000	0.0000000	11.9837197	0.0000000
hsa.miR.136.5p	1.426048	1.539528	0.5852494	1.722033	1.713813	0.2950712	1.130063	1.259715	0.6514071	-0.5919692	0.5919692	1.9664791	0.5919692	1.9664791	0.0000000	0.0000000	0.0000000	11.6576372	0.0000000
hsa.miR.192.5p	3.474000	3.723466	0.8856187	3.920081	3.942126	0.4108526	3.027920	2.831424	1.0027511	-0.8921615	0.8921615	2.9636965	0.8921615	2.9636965	0.0000000	0.0000000	0.0000000	11.4242384	0.0000000
hsa.miR.451a	2.540774	2.525599	0.6339915	2.233131	2.192706	0.4710976	2.848417	2.906464	0.6282318	0.6152860	-0.6152860	-2.0439357	-0.6152860	-2.0439357	0.0000000	0.0000000	0.0000000	11.0384525	0.0000000
hsa.miR.200a.3p	2.330223	2.419049	0.6863313	2.660594	2.674894	0.3970887	1.999851	2.171325	0.7539997	-0.6607432	0.6607432	2.1949415	0.6607432	2.1949415	0.0000000	0.0000000	0.0000000	10.4637303	0.0000000
hsa.miR.141.3p	2.470222	2.587047	0.6758787	2.787653	2.835787	0.4142754	2.152790	2.366831	0.7368061	-0.6348621	0.6348621	2.1089664	0.6348621	2.1089664	0.0000000	0.0000000	0.0000000	9.8966505	0.0000000
hsa.miR.181c.3p	1.549848	1.598609	0.3058360	1.691125	1.690791	0.2009568	1.408572	1.397065	0.3275293	-0.2825529	0.2825529	0.9386203	0.2825529	0.9386203	0.0000000	0.0000000	0.0000000	9.5661290	0.0000000
hsa.miR.30d.5p	3.824938	3.786939	0.2585958	3.705810	3.708020	0.1763818	3.944065	3.950384	0.2731545	0.2382549	-0.2382549	-0.7914657	-0.2382549	-0.7914657	0.0000000	0.0000000	0.0000000	9.5425303	0.0000000
hsa.miR.200b.3p	2.716967	2.769036	0.5121158	2.949316	3.014389	0.3627291	2.484618	2.625241	0.5351976	-0.4646977	0.4646977	1.5436922	0.4646977	1.5436922	0.0000000	0.0000000	0.0000000	9.2128238	0.0000000
hsa.miR.708.3p	1.553047	1.799718	0.7046857	1.878493	1.937453	0.3169286	1.227601	1.186108	0.8267867	-0.6508920	0.6508920	2.1622164	0.6508920	2.1622164	0.0000000	0.0000000	0.0000000	9.1585590	0.0000000
hsa.miR.210.3p	2.239766	2.271507	0.6889295	2.547543	2.542301	0.5385826	1.931988	2.106523	0.6873228	-0.6155552	0.6155552	2.0448301	0.6155552	2.0448301	0.0000000	0.0000000	0.0000000	8.9396288	0.0000000
hsa.miR.486.5p	2.102968	2.062283	0.6191482	1.830616	1.754483	0.4121882	2.375321	2.342782	0.6713086	0.5447046	-0.5447046	-1.8094696	-0.5447046	-1.8094696	0.0000000	0.0000000	0.0000000	8.4375052	0.0000000
hsa.miR.29a.3p	3.841416	3.818064	0.2415932	3.736185	3.745283	0.1796643	3.946646	3.954986	0.2503002	0.2104605	-0.2104605	-0.6991346	-0.2104605	-0.6991346	0.0000000	0.0000000	0.0000000	8.3240291	0.0000000
hsa.miR.378a.3p	2.550650	2.512377	0.3937521	2.378397	2.381114	0.2557418	2.722903	2.778885	0.4315532	0.3445063	-0.3445063	-1.1444252	-0.3445063	-1.1444252	0.0000000	0.0000000	0.0000000	8.2934009	0.0000000
hsa.miR.379.5p	2.828974	2.918613	0.4091041	3.006836	3.034753	0.2966347	2.651112	2.644205	0.4294792	-0.3557240	0.3557240	1.1816895	0.3557240	1.1816895	0.0000000	0.0000000	0.0000000	8.2616630	0.0000000
hsa.miR.141.5p	2.216028	2.392275	0.6525748	2.500775	2.556782	0.3976527	1.931282	2.148570	0.7306892	-0.5694928	0.5694928	1.8918140	0.5694928	1.8918140	0.0000000	0.0000000	0.0000000	8.1778863	0.0000000
hsa.miR.21.3p	2.950511	3.002843	0.4495447	3.143884	3.238660	0.3956108	2.757137	2.698429	0.4172376	-0.3867473	0.3867473	1.2847466	0.3867473	1.2847466	0.0000000	0.0000000	0.0000000	8.1503082	0.0000000
hsa.miR.337.3p	1.498952	1.609902	0.4286748	1.685506	1.704399	0.2599192	1.312398	1.278140	0.4810808	-0.3731072	0.3731072	1.2394354	0.3731072	1.2394354	0.0000000	0.0000000	0.0000000	8.1171714	0.0000000
hsa.miR.144.5p	1.799486	1.840358	0.7365132	1.481479	1.461856	0.4729441	2.117492	2.202314	0.8137450	0.6360122	-0.6360122	-2.1127868	-0.6360122	-2.1127868	0.0000000	0.0000000	0.0000000	8.0043727	0.0000000
hsa.miR.429	1.847904	1.950131	0.7268633	2.162646	2.205144	0.3857231	1.533162	1.702486	0.8443154	-0.6294838	0.6294838	2.0910999	0.6294838	2.0910999	0.0000000	0.0000000	0.0000000	7.8988604	0.0000000
hsa.miR.335.3p	1.773607	1.812886	0.3718545	1.932716	1.892784	0.2426583	1.614497	1.631930	0.4097115	-0.3182195	0.3182195	1.0571023	0.3182195	1.0571023	0.0000000	0.0000000	0.0000000	7.8314098	0.0000000
hsa.miR.126.5p	2.232491	2.222927	0.4152358	2.056938	2.063790	0.2104761	2.408045	2.529680	0.4898455	0.3511067	-0.3511067	-1.1663511	-0.3511067	-1.1663511	0.0000000	0.0000000	0.0000000	7.3936205	0.0000000
hsa.miR.30c.5p	2.808698	2.749100	0.3490929	2.661967	2.661797	0.1963921	2.955429	2.915562	0.4035411	0.2934616	-0.2934616	-0.9748585	-0.2934616	-0.9748585	0.0000000	0.0000000	0.0000000	7.3565035	0.0000000
hsa.miR.181a.3p	2.106380	2.174268	0.3784895	2.261578	2.305816	0.2347854	1.951183	2.028792	0.4290792	-0.3103947	0.3103947	1.0311087	0.3103947	1.0311087	0.0000000	0.0000001	0.0000001	6.9641475	0.0000000
hsa.let.7c.5p	3.419322	3.422382	0.3296842	3.287237	3.332260	0.2860501	3.551407	3.535984	0.3183740	0.2641699	-0.2641699	-0.8775535	-0.2641699	-0.8775535	0.0000000	0.0000002	0.0000001	6.7432319	0.0000000
hsa.miR.181a.5p	3.155295	3.246986	0.4050583	3.316282	3.343112	0.2324404	2.994307	2.991241	0.4725895	-0.3219750	0.3219750	1.0695778	0.3219750	1.0695778	0.0000000	0.0000004	0.0000003	6.3623836	0.0000000
hsa.miR.221.3p	2.290528	2.336670	0.3527519	2.427381	2.408816	0.2861108	2.153674	2.182603	0.3610694	-0.2737072	0.2737072	0.9092357	0.2737072	0.9092357	0.0000000	0.0000007	0.0000005	6.1577028	0.0000000
hsa.miR.93.5p	3.298589	3.328666	0.2589551	3.398683	3.400925	0.1891085	3.198495	3.236571	0.2806412	-0.2001879	0.2001879	0.6650098	0.2001879	0.6650098	0.0000000	0.0000009	0.0000006	6.0433338	0.0000000
hsa.miR.378a.5p	1.765728	1.699123	0.3998851	1.610886	1.612851	0.2430057	1.920570	1.955764	0.4624594	0.3096836	-0.3096836	-1.0287466	-0.3096836	-1.0287466	0.0000000	0.0000011	0.0000008	5.9662895	0.0000000
hsa.miR.146b.5p	2.601785	2.674141	0.4626849	2.779955	2.835954	0.2919913	2.423615	2.450139	0.5299317	-0.3563393	0.3563393	1.1837335	0.3563393	1.1837335	0.0000000	0.0000013	0.0000009	5.8990220	0.0000000
hsa.miR.23a.3p	3.411765	3.464466	0.2170216	3.494149	3.504609	0.1702973	3.329380	3.342163	0.2278979	-0.1647689	0.1647689	0.5473504	0.1647689	0.5473504	0.0000000	0.0000016	0.0000011	5.7880964	0.0000000
hsa.miR.30b.5p	2.622413	2.622930	0.3212403	2.499914	2.507222	0.2120817	2.744913	2.792110	0.3634422	0.2449988	-0.2449988	-0.8138683	-0.2449988	-0.8138683	0.0000000	0.0000017	0.0000012	5.7695073	0.0000000
hsa.miR.625.3p	2.068354	2.104397	0.3502308	2.200772	2.210917	0.2188272	1.935936	1.910435	0.4039743	-0.2648357	0.2648357	0.8797652	0.2648357	0.8797652	0.0000000	0.0000025	0.0000017	5.6075234	0.0000000
hsa.miR.182.5p	3.674023	3.755735	0.4922991	3.858145	3.842168	0.3744427	3.489902	3.616382	0.5275933	-0.3682429	0.3682429	1.2232765	0.3682429	1.2232765	0.0000000	0.0000029	0.0000020	5.5415728	0.0000001
hsa.miR.27a.3p	3.005903	3.044024	0.2647920	3.104509	3.109418	0.2287859	2.907296	2.903005	0.2625226	-0.1972135	0.1972135	0.6551290	0.1972135	0.6551290	0.0000000	0.0000030	0.0000020	5.5228315	0.0000001
hsa.miR.183.5p	3.203446	3.257163	0.4833569	3.381328	3.357706	0.3966813	3.025563	3.143805	0.4982314	-0.3557648	0.3557648	1.1818251	0.3557648	1.1818251	0.0000000	0.0000047	0.0000031	5.3289624	0.0000001
hsa.miR.181c.5p	1.665600	1.682222	0.3601516	1.795267	1.778815	0.2462991	1.535932	1.501756	0.4074728	-0.2593354	0.2593354	0.8614935	0.2593354	0.8614935	0.0000001	0.0000115	0.0000076	4.9383329	0.0000002
hsa.miR.126.3p	3.305734	3.272928	0.4223713	3.157448	3.162873	0.2190488	3.454020	3.630912	0.5158520	0.2965719	-0.2965719	-0.9851906	-0.2965719	-0.9851906	0.0000002	0.0000319	0.0000209	4.4963337	0.0000005
hsa.miR.582.3p	2.087755	2.119436	0.3376004	1.973266	1.974597	0.2964765	2.202245	2.291615	0.3386179	0.2289783	-0.2289783	-0.7606496	-0.2289783	-0.7606496	0.0000004	0.0000584	0.0000380	4.2335770	0.0000010
hsa.miR.143.3p	4.940749	4.860769	0.4133211	4.799815	4.796805	0.2682101	5.081683	4.987285	0.4808783	0.2818686	-0.2818686	-0.9363472	-0.2818686	-0.9363472	0.0000004	0.0000618	0.0000398	4.2090891	0.0000010
hsa.miR.185.5p	1.698820	1.752167	0.3122312	1.803017	1.789962	0.1825995	1.594623	1.585711	0.3750133	-0.2083937	0.2083937	0.6922687	0.2083937	0.6922687	0.0000007	0.0001204	0.0000769	3.9192525	0.0000020
hsa.miR.29c.3p	3.321214	3.327217	0.3591607	3.202955	3.215627	0.2277490	3.439473	3.491354	0.4232090	0.2365180	-0.2365180	-0.7856959	-0.2365180	-0.7856959	0.0000010	0.0001621	0.0001026	3.7900871	0.0000026
hsa.miR.223.3p	2.257390	2.288581	0.4632869	2.408097	2.462940	0.4003810	2.106684	2.111760	0.4744849	-0.3014129	0.3014129	1.0012719	0.3014129	1.0012719	0.0000011	0.0001834	0.0001149	3.7365180	0.0000029
hsa.miR.423.5p	1.545436	1.538957	0.3144486	1.443133	1.425446	0.2069216	1.647738	1.666376	0.3670736	0.2046048	-0.2046048	-0.6796823	-0.2046048	-0.6796823	0.0000013	0.0002154	0.0001337	3.6667565	0.0000034
hsa.miR.151a.5p	1.778564	1.824896	0.2355297	1.854691	1.836098	0.1493639	1.702436	1.739749	0.2783202	-0.1522549	0.1522549	0.5057800	0.1522549	0.5057800	0.0000016	0.0002604	0.0001600	3.5843739	0.0000040
hsa.let.7i.5p	2.599921	2.632392	0.2997045	2.696086	2.717300	0.1738861	2.503755	2.466912	0.3627486	-0.1923305	0.1923305	0.6389080	0.1923305	0.6389080	0.0000020	0.0003296	0.0002005	3.4820413	0.0000050
hsa.miR.26b.5p	2.777405	2.755033	0.2942712	2.683523	2.667076	0.2076405	2.871288	2.871957	0.3363026	0.1877642	-0.1877642	-0.6237392	-0.1877642	-0.6237392	0.0000020	0.0003363	0.0002026	3.4732893	0.0000050
hsa.miR.222.3p	1.679643	1.690400	0.3421027	1.788188	1.797616	0.2933599	1.571098	1.634996	0.3540146	-0.2170897	0.2170897	0.7211563	0.2170897	0.7211563	0.0000021	0.0003468	0.0002068	3.4599760	0.0000051
hsa.miR.320a.3p	2.517259	2.510587	0.2335402	2.443505	2.440882	0.2043264	2.591012	2.575436	0.2384649	0.1475073	-0.1475073	-0.4900086	-0.1475073	-0.4900086	0.0000023	0.0003863	0.0002281	3.4130330	0.0000056
hsa.miR.30e.5p	3.679150	3.640665	0.3123538	3.579560	3.581958	0.1513627	3.778740	3.843580	0.3913006	0.1991799	-0.1991799	-0.6616613	-0.1991799	-0.6616613	0.0000025	0.0004221	0.0002467	3.3745491	0.0000060
hsa.miR.200c.3p	3.479500	3.647500	0.6328315	3.679499	3.713871	0.3714689	3.279502	3.524250	0.7654977	-0.3999973	0.3999973	1.3287624	0.3999973	1.3287624	0.0000028	0.0004717	0.0002728	3.3263079	0.0000066
hsa.miR.145.5p	3.405874	3.362197	0.3557557	3.294171	3.279622	0.2492612	3.517576	3.469948	0.4086525	0.2234046	-0.2234046	-0.7421341	-0.2234046	-0.7421341	0.0000030	0.0004969	0.0002844	3.3037592	0.0000069
hsa.miR.92b.3p	1.748375	1.731752	0.3770581	1.865526	1.808052	0.2617419	1.631225	1.619889	0.4352821	-0.2343014	0.2343014	0.7783325	0.2343014	0.7783325	0.0000039	0.0006400	0.0003624	3.1938498	0.0000088
hsa.miR.629.5p	1.718671	1.767577	0.2822432	1.804344	1.819456	0.2016194	1.632997	1.650836	0.3234272	-0.1713470	0.1713470	0.5692024	0.1713470	0.5692024	0.0000064	0.0010697	0.0005993	2.9707322	0.0000145
hsa.miR.99a.5p	2.916024	2.912899	0.3862114	2.800660	2.801168	0.3181101	3.031388	3.020665	0.4143220	0.2307282	-0.2307282	-0.7664624	-0.2307282	-0.7664624	0.0000086	0.0014262	0.0007904	2.8458122	0.0000190
hsa.miR.22.3p	4.901288	4.935034	0.2599745	4.979132	4.983023	0.1344526	4.823443	4.825832	0.3248074	-0.1556883	0.1556883	0.5171853	0.1556883	0.5171853	0.0000101	0.0016706	0.0009158	2.7771206	0.0000220
hsa.miR.10b.5p	4.284825	4.160990	0.6577961	4.092498	4.126032	0.2208435	4.477153	4.339191	0.8637267	0.3846552	-0.3846552	-1.2777969	-0.3846552	-1.2777969	0.0000184	0.0030501	0.0016537	2.5156825	0.0000396
hsa.miR.142.3p	2.908082	2.993345	0.5523317	3.062898	3.069081	0.3324835	2.753266	2.754739	0.6738583	-0.3096321	0.3096321	1.0285755	0.3096321	1.0285755	0.0000350	0.0058148	0.0031176	2.2354673	0.0000745
hsa.miR.16.5p	2.418426	2.396977	0.2678058	2.344887	2.354009	0.1520643	2.491965	2.532161	0.3317754	0.1470782	-0.1470782	-0.4885833	-0.1470782	-0.4885833	0.0000518	0.0086050	0.0045617	2.0652508	0.0001089
hsa.miR.10a.5p	4.453193	4.572159	0.4172756	4.567356	4.619375	0.2726925	4.339031	4.448143	0.4992066	-0.2283251	0.2283251	0.7584795	0.2283251	0.7584795	0.0000528	0.0087721	0.0045974	2.0568959	0.0001097
hsa.miR.365a.3p	1.558982	1.524607	0.3288053	1.472455	1.482687	0.2603646	1.645509	1.646930	0.3665257	0.1730535	-0.1730535	-0.5748714	-0.1730535	-0.5748714	0.0000972	0.0161318	0.0083574	1.7923179	0.0001970
hsa.miR.365b.3p	1.559072	1.524607	0.3286232	1.472600	1.482687	0.2598729	1.645545	1.646930	0.3665720	0.1729456	-0.1729456	-0.5745130	-0.1729456	-0.5745130	0.0000973	0.0161562	0.0083574	1.7916615	0.0001970
hsa.miR.20a.5p	2.167170	2.188072	0.3531756	2.258504	2.252491	0.2151305	2.075836	2.092815	0.4330362	-0.1826683	0.1826683	0.6068109	0.1826683	0.6068109	0.0001387	0.0230266	0.0116520	1.6377698	0.0002774
hsa.miR.195.5p	1.610326	1.644712	0.4593292	1.492892	1.530241	0.2351047	1.727760	1.829698	0.5838159	0.2348685	-0.2348685	-0.7802161	-0.2348685	-0.7802161	0.0001727	0.0286635	0.0143318	1.5426701	0.0003412
hsa.miR.26a.5p	3.363368	3.336961	0.2249507	3.307628	3.297116	0.1471895	3.419108	3.407502	0.2715615	0.1114806	-0.1114806	-0.3703306	-0.1114806	-0.3703306	0.0002606	0.0432635	0.0213711	1.3638783	0.0005090
hsa.miR.145.3p	1.779374	1.754841	0.2975307	1.706504	1.693139	0.2239980	1.852244	1.840403	0.3420364	0.1457395	-0.1457395	-0.4841363	-0.1457395	-0.4841363	0.0002988	0.0495960	0.0242005	1.3045533	0.0005767
hsa.miR.142.5p	1.517108	1.642632	0.7709832	1.707036	1.728336	0.3336782	1.327180	1.413437	1.0051222	-0.3798562	0.3798562	1.2618548	0.3798562	1.2618548	0.0003066	0.0509030	0.0245316	1.2932569	0.0005851
hsa.miR.155.5p	2.133480	2.195366	0.4195203	2.233687	2.297068	0.3475670	2.033272	2.006969	0.4610634	-0.2004154	0.2004154	0.6657657	0.2004154	0.6657657	0.0004167	0.0691679	0.0329172	1.1600957	0.0007860
hsa.let.7d.5p	2.204108	2.185887	0.2122742	2.154807	2.147458	0.1420691	2.253409	2.269843	0.2558420	0.0986016	-0.0986016	-0.3275473	-0.0986016	-0.3275473	0.0006292	0.1044446	0.0490764	0.9811142	0.0011735
hsa.miR.101.3p	4.064812	4.041831	0.3932389	3.975163	3.934040	0.1680979	4.154461	4.258030	0.5159943	0.1792983	-0.1792983	-0.5956161	-0.1792983	-0.5956161	0.0008471	0.1406149	0.0652250	0.8519688	0.0015624
hsa.miR.15a.5p	1.962872	1.985385	0.2869339	2.027709	2.007988	0.1768348	1.898034	1.940992	0.3545154	-0.1296752	0.1296752	0.4307717	0.1296752	0.4307717	0.0008984	0.1491266	0.0678151	0.8264448	0.0016209
hsa.miR.140.3p	3.000561	3.018035	0.2271711	2.949429	2.935298	0.2005767	3.051693	3.090265	0.2412282	0.1022638	-0.1022638	-0.3397129	-0.1022638	-0.3397129	0.0008923	0.1481224	0.0678151	0.8293794	0.0016209
hsa.miR.193a.5p	2.336431	2.300347	0.3276854	2.266929	2.278125	0.1938504	2.405932	2.378371	0.4104126	0.1390021	-0.1390021	-0.4617551	-0.1390021	-0.4617551	0.0018588	0.3085666	0.1375538	0.5106511	0.0033179
hsa.let.7b.5p	4.195831	4.209035	0.2924159	4.256938	4.282751	0.1889508	4.134724	4.104211	0.3585804	-0.1222138	0.1222138	0.4059855	0.1222138	0.4059855	0.0021512	0.3570954	0.1570359	0.4472157	0.0037989
hsa.miR.425.5p	1.923042	1.930834	0.3243793	1.987356	1.978949	0.2395357	1.858729	1.880977	0.3817182	-0.1286263	0.1286263	0.4272874	0.1286263	0.4272874	0.0035774	0.5938450	0.2575713	0.2263269	0.0062510
hsa.miR.99b.5p	4.315202	4.300285	0.2601134	4.263737	4.282048	0.1951765	4.366667	4.343604	0.3041630	0.1029303	-0.1029303	-0.3419271	-0.1029303	-0.3419271	0.0036421	0.6045962	0.2585923	0.2185346	0.0062979
hsa.miR.146b.3p	1.886946	1.965307	0.4754291	1.979342	1.993235	0.3044790	1.794549	1.860622	0.5867326	-0.1847929	0.1847929	0.6138687	0.1847929	0.6138687	0.0043674	0.7249845	0.3057163	0.1396713	0.0074741
hsa.miR.128.3p	1.955925	1.943604	0.2304255	2.000480	1.993252	0.1994596	1.911370	1.897153	0.2508004	-0.0891101	0.0891101	0.2960174	0.0891101	0.2960174	0.0044531	0.7392212	0.3072666	0.1312256	0.0075431
hsa.miR.34a.5p	2.074666	2.121651	0.2675331	2.125712	2.136585	0.1931050	2.023620	2.059319	0.3182343	-0.1020923	0.1020923	0.3391431	0.1020923	0.3391431	0.0050922	0.8453067	0.3462702	0.0729857	0.0085385
hsa.miR.1307.5p	2.032668	2.074195	0.4746939	2.121558	2.143052	0.3137240	1.943777	1.930948	0.5817384	-0.1777808	0.1777808	0.5905749	0.1777808	0.5905749	0.0060341	1.0000000	0.4042856	0.0000000	0.0100166
hsa.miR.146a.5p	1.834930	1.878293	0.5428638	1.936147	1.968467	0.3763981	1.733712	1.804289	0.6556095	-0.2024345	0.2024345	0.6724729	0.2024345	0.6724729	0.0062340	1.0000000	0.4114442	0.0000000	0.0102460
hsa.miR.660.5p	1.637156	1.706445	0.5648980	1.742335	1.736172	0.1929619	1.531977	1.656099	0.7626676	-0.2103579	0.2103579	0.6987938	0.2103579	0.6987938	0.0065781	1.0000000	0.4275745	0.0000000	0.0107055
hsa.miR.1307.3p	2.668366	2.682073	0.3103661	2.725068	2.712113	0.1957961	2.611663	2.652759	0.3856627	-0.1134058	0.1134058	0.3767259	0.1134058	0.3767259	0.0074280	1.0000000	0.4753900	0.0000000	0.0119713
hsa.miR.17.3p	2.280466	2.310070	0.2760079	2.330198	2.324300	0.1630184	2.230733	2.251456	0.3485844	-0.0994646	0.0994646	0.3304142	0.0994646	0.3304142	0.0083333	1.0000000	0.5249975	0.0000000	0.0133012
hsa.miR.103a.3p	4.078473	4.104653	0.2058716	4.115271	4.122395	0.1680536	4.041675	4.049734	0.2327882	-0.0735962	0.0735962	0.2444812	0.0735962	0.2444812	0.0086789	1.0000000	0.5380907	0.0000000	0.0137209
hsa.miR.484	1.597652	1.580193	0.2719205	1.550795	1.553409	0.1598979	1.644510	1.656175	0.3443530	0.0937157	-0.0937157	-0.3113168	-0.0937157	-0.3113168	0.0116710	1.0000000	0.7119329	0.0000000	0.0182773
hsa.miR.452.5p	1.609759	1.684291	0.4772755	1.691423	1.719895	0.2895699	1.528095	1.619481	0.6003483	-0.1633282	0.1633282	0.5425647	0.1633282	0.5425647	0.0122598	1.0000000	0.7355852	0.0000000	0.0189271
hsa.miR.584.5p	1.562512	1.609699	0.4055066	1.631695	1.617142	0.3258710	1.493330	1.570896	0.4632148	-0.1383646	0.1383646	0.4596372	0.1383646	0.4596372	0.0123140	1.0000000	0.7355852	0.0000000	0.0189271
hsa.miR.9.5p	2.452682	2.417320	0.5298502	2.364790	2.362214	0.3600516	2.540574	2.612118	0.6472233	0.1757844	-0.1757844	-0.5839430	-0.1757844	-0.5839430	0.0151165	1.0000000	0.8767577	0.0000000	0.0230215
hsa.miR.361.3p	2.114070	2.138671	0.2668813	2.157051	2.182644	0.1719882	2.071090	2.091288	0.3313815	-0.0859613	0.0859613	0.2855574	0.0859613	0.2855574	0.0184170	1.0000000	1.0000000	0.0000000	0.0277930
hsa.let.7g.5p	2.743360	2.731598	0.2633678	2.701240	2.687710	0.2007329	2.785480	2.824734	0.3090374	0.0842401	-0.0842401	-0.2798397	-0.0842401	-0.2798397	0.0191012	1.0000000	1.0000000	0.0000000	0.0285658
hsa.let.7a.3p	1.362918	1.456311	0.5840349	1.454096	1.472496	0.2172292	1.271740	1.413722	0.7883141	-0.1823566	0.1823566	0.6057754	0.1823566	0.6057754	0.0227488	1.0000000	1.0000000	0.0000000	0.0337170
hsa.miR.28.3p	3.478699	3.452430	0.2371295	3.442283	3.445475	0.2164372	3.515115	3.488616	0.2519303	0.0728325	-0.0728325	-0.2419443	-0.0728325	-0.2419443	0.0243409	1.0000000	1.0000000	0.0000000	0.0355939
hsa.miR.23b.3p	3.145549	3.139008	0.1654088	3.120156	3.106189	0.1396735	3.170942	3.185124	0.1848453	0.0507862	-0.0507862	-0.1687082	-0.0507862	-0.1687082	0.0244440	1.0000000	1.0000000	0.0000000	0.0355939
hsa.miR.29b.3p	2.730065	2.739194	0.3702233	2.785646	2.771371	0.2357865	2.674484	2.713670	0.4621597	-0.1111620	0.1111620	0.3692721	0.1111620	0.3692721	0.0281053	1.0000000	1.0000000	0.0000000	0.0405694

Let’s visualize the results of differential expression using heatmap and vulcano plot.

OmicSelector_heatmap(x = dplyr::select(trainx, sig_de$miR), rlab = data.frame(Class = train$Class), zscore = F, margins = c(10, 10))

Z-scoring the values before clustering and plotting will help us to gain more insight.

OmicSelector_heatmap(x = dplyr::select(trainx, sig_de$miR), rlab = data.frame(Class = train$Class), zscore = T, margins = c(10, 10))

We will also create a vulcano plot and label top 10 most significant miRNAs:

OmicSelector_vulcano_plot(selected_miRNAs = de$miR, DE = de, only_label = sig_de$miR[1:10])

We may also what to check the consistency of differential expression between datasets:

de_test = OmicSelector_differential_expression_ttest(dplyr::select(test, starts_with("hsa")), test$Class)
de_valid = OmicSelector_differential_expression_ttest(dplyr::select(valid, starts_with("hsa")), valid$Class)
OmicSelector_correlation_plot(de$log2FC, de_test$log2FC, "log2FC on training set", "log2FC on test set", "", yx = T)

OmicSelector_correlation_plot(de$log2FC, de_valid$log2FC, "log2FC on training set", "log2FC on validation set", "", yx = T)

OmicSelector_correlation_plot(de_test$log2FC, de_valid$log2FC, "log2FC on test set", "log2FC on validation set", "", yx = T)

5 miRNA selection

The main feature of this package is the shotgun-like feature selection evaluation of possible miRNA signatures of biological processes. The function can be applied in a straightforward way, e.g.:

selected_features = OmicSelector_OmicSelector(wd = getwd(), m = 1:10, max_iterations = 1, stamp = "tutorial")  # we just run only first 10 methods for the sake of speed.

But, for largers projects we suggest using the following wrapper wich will perform the feature selection in parallel, significantly reducing computational time. We do not recommend using more than 5 threads, beacuse some of the methods inhereditly use multicore processing:

readLines("Tutorial_OmicSelector.R") %>% paste0(collapse = "\n") %>% cat
#> #options(warn = -1)
#> suppressMessages(library(foreach))
#> suppressMessages(library(doParallel))
#> suppressMessages(library(parallel))
#> suppressMessages(library(doParallel))
#> 
#> m = 1:56 # which methods to check?
#> 
#> cl <- makePSOCKcluster(useXDR = TRUE, 5) # We do not recommend using more than 5 threads, beacuse some of the methods inhereditly use multicore processing.
#> doParallel:: registerDoParallel(cl)
#> iterations = length(m)
#> pb <- txtProgressBar(max = iterations, style = 3)
#> progress <- function(n) setTxtProgressBar(pb, n)
#> opts <- list(progress = progress)
#> foreach(i = m, .options.snow = opts) %dopar%
#> {
#>   suppressMessages(library(OmicSelector))
#>   # setwd("/OmicSelector/OmicSelector/vignettes") # change it you to your working directory
#>   OmicSelector_OmicSelector(m = i, max_iterations = 1, stamp = "tutorial", debug = F, # we set debug to false (to make the package smaller), you may also want to change stamp to something meaningful, max_iterations was set to 1 to recude the computational time.. in real life scenarios it is resonable to use at least 10 iterations.
#>                   prefer_no_features = 11, # Few methods are filter rather than wrapper methods, thus requires the maximum number of maximum features.
#>                   conda_path = "/opt/conda/bin/conda", # Methods line WxNet requires usage of python. In setup script we create conda enviorment. Providing conda_path makes it easier to activate env. We prefer this apporach over use_condaenv.
#>                   timeout = 600) # We don't want to wait eternity in this tutorial, just 10 minutes. Timeout is useful for complicated methods. Depending on your CPU 2 days may be reasonable for larger projects. Note that some methods cannot be controled with timeout parameter.
#> }
#> 
#> stopCluster(cl)
#> #options(warn = 0)

If you are using our enviorment to learn this package you can tweak and run this code in the interactive notebook. Click here.

A few notes about what is does:

• This function iterates though available methods which are described by m parameter. The aim of this function is to perform feature selection using multiple methods and to create formulas for benchmarking.
• It loads the data from working directory. The output is mainly put in files in the working directory. Log and temporary files are placed in a created temp subfolder.

Files created for each method (e.g. for stamp=tutorial and m=1):

• formulastutorial-1.RDS - main result file containing the final formula (final set of miRNAs selected by this method).
• time1-formula.RDS - time taken to compute the results
• tutorial1featureselection.log - log file of the process
• (optional) all1-tutorial.rdata - all variables created during feature selection (created if debug=T).

Pearls about the methods:

• Sig = miRNAs with p-value <0.05 after BH correction (DE using t-test)
• Fcsig = sig + absolute log2FC filter (included if abs. log2FC>1)
• Cfs = Correlation-based Feature Selection for Machine Learning (more: https://www.cs.waikato.ac.nz/~mhall/thesis.pdf)
• Classloop = Classification using different classification algorithms (classifiers) with the embedded feature selection and using the different schemes for the performance validation (more: https://rdrr.io/cran/Biocomb/man/classifier.loop.html)
• Fcfs = CFS algorithm with forward search (https://rdrr.io/cran/Biocomb/man/select.forward.Corr.html)
• MDL methods = minimal description length (MDL) discretization algorithm with different a method of feature ranking or feature selection (AUC, SU, CorrSF) (more: https://rdrr.io/cran/Biocomb/man/select.process.html)
• bounceR = genetic algorithm with componentwise boosting (more: https://www.statworx.com/ch/blog/automated-feature-selection-using-bouncer/)
• RandomForestRFE = recursive feature elimination using random forest with resampling to assess the performance. (more: https://topepo.github.io/caret/recursive-feature-elimination.html#resampling-and-external-validation)
• GeneticAlgorithmRF (more: https://topepo.github.io/caret/feature-selection-using-genetic-algorithms.html)
• SimulatedAnnealing = makes small random changes (i.e. perturbations) to an initial candidate solution (more: https://topepo.github.io/caret/feature-selection-using-simulated-annealing.html)
• Boruta (more: https://www.jstatsoft.org/article/view/v036i11/v36i11.pdf)
• spFSR = simultaneous perturbation stochastic approximation (SPSA-FSR) (more: https://arxiv.org/abs/1804.05589)
• varSelRF = using the out-of-bag error as minimization criterion, carry out variable elimination from random forest, by successively eliminating the least important variables (with importance as returned from random forest). (more: https://www.ncbi.nlm.nih.gov/pubmed/16398926)
• WxNet = a neural network-based feature selection algorithm for transcriptomic data (more: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642261/)
• Step = backward stepwise method of feature selection based on logistic regression (GLM, family = binomial) using AIC criteria (stepAIC) and functions from My.stepwise package (https://cran.r-project.org/web/packages/My.stepwise/index.html)

Notes about methods:

Comming soon…

The OmicSelector functions saves all output files to temp/ directory. As users may want to run multiple selection methods in different configurations, we do not recommend using the return of this function in the following steps. Instead, we provide OmicSelector_merge_formulas() which conviniently summerizes the results of feature selection. We can do:

selected_sets_of_miRNAs = OmicSelector_merge_formulas(max_miRNAs = 11)  # we filter out sets with more than 11 miRNAs.
selected_sets_of_miRNAs_with_own = OmicSelector_merge_formulas(max_miRNAs = 11, add = list(my_own_signature = c("hsa.miR.192.5p", "hsa.let.7g.5p", "hsa.let.7a.5p", 
    "hsa.let.7d.5p", "hsa.miR.194.5p", "hsa.miR.98.5p", "hsa.let.7f.5p", "hsa.miR.26b.5p")))  # you can also add your own signature (for example selected from literature)

Note that:

• Two files are created in working directory: (1) featureselection_formulas_all.RDS - contains the formulas for all selection methods, (2) featureselection_formulas_final.RDS - contains methods that selected smaller or equal number of microRNAs than specified in max_miRNA parameter, as well as fcsig and cfs_sig.
• The results of fcsig and cfs_sig methods are always retained in the final formulas set (ignoring max_miRNA parameter) - they are commonly used as benchmark comparator for the final set of miRNAs. Those sets can be manually removed (if needed) from final selection.
• Readable tables are written in corresponding *.csv files.

Let’s analyze the process of feature selection:

all_sets = readRDS("featureselection_formulas_all.RDS")
length(all_sets)  # How many feature selection methods completed in time?
#> [1] 23
final_sets = readRDS("featureselection_formulas_final.RDS")
length(final_sets)  # How many feature selection methods completed in time and fulfilled max_miRNA criteria? (remember about fcsig and cfs_sig)
#> [1] 14
featureselection_formulas_final = fread("featureselection_formulas_final.csv")
OmicSelector_table(featureselection_formulas_final)  # show information about selected formulas

name	formula	ile_miRNA
cfs_sig	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p	34
fcsig	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p	50
my_own_signature	Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p	0
sigtop	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p	11
sigtopBonf	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p	11
sigtopHolm	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p	11
topFC	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p	11
sigtopSMOTE	Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p	11
sigtopBonfSMOTE	Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p	11
sigtopHolmSMOTE	Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p	11
topFCSMOTE	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p	11
cfsSMOTE	Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p	5
cfsSMOTE_sig	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p	5
fcfsSMOTE	Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.708.3p + hsa.miR.375.3p + hsa.miR.30e.3p	5

Note that my_own_signture has 0 miRNAs according to the table. This trick is done to make sure that signatures added manually will not be filtered out based on max_miRNA parameter.

Now, we will summarize number of microRNAs selected by methods implemented in OmicSelector_OmicSelector by creating histogram and calculating some descriptive statistics.

hist(featureselection_formulas_final$ile_miRNA[-which(featureselection_formulas_final$ile_miRNA == 0)], breaks = ncol(train), main = "Number of selected microRNAs distribution", 
    xlab = "Number of selected microRNAs")  # Histogram showing how many miRNAs were selected in final set.

psych::describe(featureselection_formulas_final$ile_miRNA[-which(featureselection_formulas_final$ile_miRNA == 0)])  # Descriptive statistics of how many features where selected in the final set.
#>    vars  n  mean    sd median trimmed mad min max range skew kurtosis   se
#> X1    1 13 14.38 12.94     11      12   0   5  50    45 1.77     1.89 3.59

6 Benchmarking

In the next step of looking for the best microRNA signature, we perform benchmarking. This tests all the signatures using different classifier architectures. Here is the example of benchmark with default parameters:

readLines("Tutorial_benchmark.R") %>% paste0(collapse = "\n") %>% cat

If you are using our enviorment to learn this package you can tweak and run this code in the interactive notebook. Click here.

Just for rendering this tutorial we will use a very simple benchmark using only logistic regression and conditional trees.

OmicSelector_benchmark(search_iters = 5, # 5 random hyperparameter sets will be checked; 5 is set here for speed purposes.. for real projects use more, like 5000...
            algorithms = c("ctree"), # just add ctree, note that logistic regression (glm) is always included
            output_file = paste0("benchmark.csv")) # the main output
#>              method SMOTE
#> 1           cfs_sig    No
#> 2             fcsig    No
#> 3  my_own_signature    No
#> 4            sigtop    No
#> 5        sigtopBonf    No
#> 6        sigtopHolm    No
#> 7             topFC    No
#> 8       sigtopSMOTE   Yes
#> 9   sigtopBonfSMOTE   Yes
#> 10  sigtopHolmSMOTE   Yes
#> 11       topFCSMOTE   Yes
#> 12         cfsSMOTE   Yes
#> 13     cfsSMOTE_sig   Yes
#> 14        fcfsSMOTE   Yes
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      miRy
#> 1                                                                                                                                                                                                                                                                                       Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + \n    hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p
#> 2  Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + \n    hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p
#> 3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p
#> 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 7                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
#> 8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
#> 12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p
#> 13                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p
#> 14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.708.3p + hsa.miR.375.3p + hsa.miR.30e.3p
#>    glm_modelname glm_train_ROCAUC glm_train_ROCAUC_lower95CI
#> 1     1589408746        1.0000000                          1
#> 2     1589408757        1.0000000                          1
#> 3     1589408768        0.9239235          0.890138639558989
#> 4     1589408779        0.9961569          0.990219096927101
#> 5     1589408789        0.9961569          0.990219096927101
#> 6     1589408800        0.9961569          0.990219096927101
#> 7     1589408810        0.9939733          0.985662071431939
#> 8     1589408820        0.9954188          0.994886530432955
#> 9     1589408845        0.9954188          0.994886530432955
#> 10    1589408870        0.9954188          0.994886530432955
#> 11    1589408897        0.9977293          0.997300123062692
#> 12    1589408921        0.9971039          0.996457027614093
#> 13    1589408941        0.9971039          0.996457027614093
#> 14    1589408964        0.9971039          0.996457027614093
#>    glm_train_ROCAUC_upper95CI glm_train_Accuracy glm_train_Sensitivity
#> 1                           1          1.0000000             1.0000000
#> 2                           1          1.0000000             1.0000000
#> 3           0.957708333975817          0.8317757             0.8504673
#> 4                           1          0.9859813             1.0000000
#> 5                           1          0.9859813             1.0000000
#> 6                           1          0.9859813             1.0000000
#> 7                           1          0.9813084             0.9906542
#> 8           0.995951097307459          0.9748454             0.9731776
#> 9           0.995951097307459          0.9748454             0.9731776
#> 10          0.995951097307459          0.9748454             0.9731776
#> 11          0.998158531720596          0.9912587             1.0000000
#> 12          0.997750828318674          0.9839587             0.9811215
#> 13          0.997750828318674          0.9839587             0.9811215
#> 14          0.997750828318674          0.9839587             0.9811215
#>    glm_train_Specificity glm_test_Accuracy glm_test_Sensitivity
#> 1              1.0000000         0.8888889            0.9166667
#> 2              1.0000000         0.9166667            0.9166667
#> 3              0.8130841         0.8472222            0.8055556
#> 4              0.9719626         0.9444444            1.0000000
#> 5              0.9719626         0.9444444            1.0000000
#> 6              0.9719626         0.9444444            1.0000000
#> 7              0.9719626         0.9444444            1.0000000
#> 8              0.9764967         0.8888889            0.9166667
#> 9              0.9764967         0.8888889            0.9166667
#> 10             0.9764967         0.8888889            0.9166667
#> 11             0.9826039         0.9444444            1.0000000
#> 12             0.9867678         0.9305556            0.9722222
#> 13             0.9867678         0.9305556            0.9722222
#> 14             0.9867678         0.9305556            0.9722222
#>    glm_test_Specificity glm_valid_Accuracy glm_valid_Sensitivity
#> 1             0.8611111          1.0000000             1.0000000
#> 2             0.9166667          0.9571429             1.0000000
#> 3             0.8888889          0.8857143             0.8857143
#> 4             0.8888889          0.9714286             1.0000000
#> 5             0.8888889          0.9714286             1.0000000
#> 6             0.8888889          0.9714286             1.0000000
#> 7             0.8888889          0.9857143             1.0000000
#> 8             0.8611111          0.9714286             1.0000000
#> 9             0.8611111          0.9714286             1.0000000
#> 10            0.8611111          0.9714286             1.0000000
#> 11            0.8888889          0.9857143             1.0000000
#> 12            0.8888889          0.9857143             1.0000000
#> 13            0.8888889          0.9857143             1.0000000
#> 14            0.8888889          0.9857143             1.0000000
#>    glm_valid_Specificity ctree_modelname ctree_train_ROCAUC
#> 1              1.0000000      1589409024          0.9768539
#> 2              0.9142857      1589409035          0.9943663
#> 3              0.8857143      1589409047          0.9753254
#> 4              0.9428571      1589409058          0.9905232
#> 5              0.9428571      1589409070          0.9905232
#> 6              0.9428571      1589409082          0.9905232
#> 7              0.9714286      1589409093          0.9944537
#> 8              0.9428571      1589409105          0.9999357
#> 9              0.9428571      1589409129          0.9999357
#> 10             0.9428571      1589409151          0.9999357
#> 11             0.9714286      1589409176          0.9999653
#> 12             0.9714286      1589409197          0.9995422
#> 13             0.9714286      1589409218          0.9995422
#> 14             0.9714286      1589409238          0.9995422
#>    ctree_train_ROCAUC_lower95CI ctree_train_ROCAUC_upper95CI
#> 1             0.956749862266401            0.996957885135119
#> 2             0.989250362911224            0.999482277494052
#> 3             0.960566402099731            0.990084309752833
#> 4             0.979470550029621                            1
#> 5             0.979470550029621                            1
#> 6             0.979470550029621                            1
#> 7             0.989338017532758            0.999569310618172
#> 8             0.999845878128999                            1
#> 9             0.999845878128999                            1
#> 10            0.999845878128999                            1
#> 11            0.999902047822822                            1
#> 12            0.999363841491172            0.999720535284351
#> 13            0.999363841491172            0.999720535284351
#> 14            0.999363841491172            0.999720535284351
#>    ctree_train_Accuracy ctree_train_Sensitivity ctree_train_Specificity
#> 1             0.9485981               0.9813084               0.9158879
#> 2             0.9579439               0.9345794               0.9813084
#> 3             0.8971963               0.8317757               0.9626168
#> 4             0.9579439               0.9345794               0.9813084
#> 5             0.9579439               0.9345794               0.9813084
#> 6             0.9579439               0.9345794               0.9813084
#> 7             0.9579439               0.9906542               0.9252336
#> 8             0.9993955               1.0000000               0.9987971
#> 9             0.9993955               1.0000000               0.9987971
#> 10            0.9993955               1.0000000               0.9987971
#> 11            0.9996745               1.0000000               0.9993523
#> 12            0.9981866               1.0000000               0.9963912
#> 13            0.9981866               1.0000000               0.9963912
#> 14            0.9981866               1.0000000               0.9963912
#>    ctree_test_Accuracy ctree_test_Sensitivity ctree_test_Specificity
#> 1            0.9305556              1.0000000              0.8611111
#> 2            0.9166667              0.9444444              0.8888889
#> 3            0.7916667              0.6944444              0.8888889
#> 4            0.9166667              0.9444444              0.8888889
#> 5            0.9166667              0.9444444              0.8888889
#> 6            0.9166667              0.9444444              0.8888889
#> 7            0.9305556              0.9722222              0.8888889
#> 8            0.8611111              0.7500000              0.9722222
#> 9            0.8611111              0.7500000              0.9722222
#> 10           0.8611111              0.7500000              0.9722222
#> 11           0.9444444              0.8888889              1.0000000
#> 12           0.9444444              0.9444444              0.9444444
#> 13           0.9444444              0.9444444              0.9444444
#> 14           0.9444444              0.9444444              0.9444444
#>    ctree_valid_Accuracy ctree_valid_Sensitivity ctree_valid_Specificity
#> 1             0.9571429               1.0000000               0.9142857
#> 2             0.9571429               0.9714286               0.9428571
#> 3             0.8714286               0.8000000               0.9428571
#> 4             0.9571429               0.9714286               0.9428571
#> 5             0.9571429               0.9714286               0.9428571
#> 6             0.9571429               0.9714286               0.9428571
#> 7             0.9714286               1.0000000               0.9428571
#> 8             0.9428571               0.8857143               1.0000000
#> 9             0.9428571               0.8857143               1.0000000
#> 10            0.9428571               0.8857143               1.0000000
#> 11            0.9571429               0.9142857               1.0000000
#> 12            0.9571429               0.9428571               0.9714286
#> 13            0.9571429               0.9428571               0.9714286
#> 14            0.9571429               0.9428571               0.9714286

As benchmarking is done, the main result file is saved in file specified in output_file parameter. It contains the performance metrics of signatures satisfying initial criteria (e.g. max_miRNA) across different methods of modelling. Let’s take a quick look:

OmicSelector_table(fread("benchmark.csv"))

V1	method	SMOTE	miRy	glm_modelname	glm_train_ROCAUC	glm_train_ROCAUC_lower95CI	glm_train_ROCAUC_upper95CI	glm_train_Accuracy	glm_train_Sensitivity	glm_train_Specificity	glm_test_Accuracy	glm_test_Sensitivity	glm_test_Specificity	glm_valid_Accuracy	glm_valid_Sensitivity	glm_valid_Specificity	ctree_modelname	ctree_train_ROCAUC	ctree_train_ROCAUC_lower95CI	ctree_train_ROCAUC_upper95CI	ctree_train_Accuracy	ctree_train_Sensitivity	ctree_train_Specificity	ctree_test_Accuracy	ctree_test_Sensitivity	ctree_test_Specificity	ctree_valid_Accuracy	ctree_valid_Sensitivity	ctree_valid_Specificity
1	cfs_sig	No	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p	1589408746	1.0000000	1.0000000	1.0000000	1.0000000	1.0000000	1.0000000	0.8888889	0.9166667	0.8611111	1.0000000	1.0000000	1.0000000	1589409024	0.9768539	0.9567499	0.9969579	0.9485981	0.9813084	0.9158879	0.9305556	1.0000000	0.8611111	0.9571429	1.0000000	0.9142857
2	fcsig	No	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p	1589408757	1.0000000	1.0000000	1.0000000	1.0000000	1.0000000	1.0000000	0.9166667	0.9166667	0.9166667	0.9571429	1.0000000	0.9142857	1589409035	0.9943663	0.9892504	0.9994823	0.9579439	0.9345794	0.9813084	0.9166667	0.9444444	0.8888889	0.9571429	0.9714286	0.9428571
3	my_own_signature	No	Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p	1589408768	0.9239235	0.8901386	0.9577083	0.8317757	0.8504673	0.8130841	0.8472222	0.8055556	0.8888889	0.8857143	0.8857143	0.8857143	1589409047	0.9753254	0.9605664	0.9900843	0.8971963	0.8317757	0.9626168	0.7916667	0.6944444	0.8888889	0.8714286	0.8000000	0.9428571
4	sigtop	No	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p	1589408779	0.9961569	0.9902191	1.0000000	0.9859813	1.0000000	0.9719626	0.9444444	1.0000000	0.8888889	0.9714286	1.0000000	0.9428571	1589409058	0.9905232	0.9794706	1.0000000	0.9579439	0.9345794	0.9813084	0.9166667	0.9444444	0.8888889	0.9571429	0.9714286	0.9428571
5	sigtopBonf	No	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p	1589408789	0.9961569	0.9902191	1.0000000	0.9859813	1.0000000	0.9719626	0.9444444	1.0000000	0.8888889	0.9714286	1.0000000	0.9428571	1589409070	0.9905232	0.9794706	1.0000000	0.9579439	0.9345794	0.9813084	0.9166667	0.9444444	0.8888889	0.9571429	0.9714286	0.9428571
6	sigtopHolm	No	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p	1589408800	0.9961569	0.9902191	1.0000000	0.9859813	1.0000000	0.9719626	0.9444444	1.0000000	0.8888889	0.9714286	1.0000000	0.9428571	1589409082	0.9905232	0.9794706	1.0000000	0.9579439	0.9345794	0.9813084	0.9166667	0.9444444	0.8888889	0.9571429	0.9714286	0.9428571
7	topFC	No	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p	1589408810	0.9939733	0.9856621	1.0000000	0.9813084	0.9906542	0.9719626	0.9444444	1.0000000	0.8888889	0.9857143	1.0000000	0.9714286	1589409093	0.9944537	0.9893380	0.9995693	0.9579439	0.9906542	0.9252336	0.9305556	0.9722222	0.8888889	0.9714286	1.0000000	0.9428571
8	sigtopSMOTE	Yes	Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p	1589408820	0.9954188	0.9948865	0.9959511	0.9748454	0.9731776	0.9764967	0.8888889	0.9166667	0.8611111	0.9714286	1.0000000	0.9428571	1589409105	0.9999357	0.9998459	1.0000000	0.9993955	1.0000000	0.9987971	0.8611111	0.7500000	0.9722222	0.9428571	0.8857143	1.0000000
9	sigtopBonfSMOTE	Yes	Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p	1589408845	0.9954188	0.9948865	0.9959511	0.9748454	0.9731776	0.9764967	0.8888889	0.9166667	0.8611111	0.9714286	1.0000000	0.9428571	1589409129	0.9999357	0.9998459	1.0000000	0.9993955	1.0000000	0.9987971	0.8611111	0.7500000	0.9722222	0.9428571	0.8857143	1.0000000
10	sigtopHolmSMOTE	Yes	Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p	1589408870	0.9954188	0.9948865	0.9959511	0.9748454	0.9731776	0.9764967	0.8888889	0.9166667	0.8611111	0.9714286	1.0000000	0.9428571	1589409151	0.9999357	0.9998459	1.0000000	0.9993955	1.0000000	0.9987971	0.8611111	0.7500000	0.9722222	0.9428571	0.8857143	1.0000000
11	topFCSMOTE	Yes	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p	1589408897	0.9977293	0.9973001	0.9981585	0.9912587	1.0000000	0.9826039	0.9444444	1.0000000	0.8888889	0.9857143	1.0000000	0.9714286	1589409176	0.9999653	0.9999020	1.0000000	0.9996745	1.0000000	0.9993523	0.9444444	0.8888889	1.0000000	0.9571429	0.9142857	1.0000000
12	cfsSMOTE	Yes	Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p	1589408921	0.9971039	0.9964570	0.9977508	0.9839587	0.9811215	0.9867678	0.9305556	0.9722222	0.8888889	0.9857143	1.0000000	0.9714286	1589409197	0.9995422	0.9993638	0.9997205	0.9981866	1.0000000	0.9963912	0.9444444	0.9444444	0.9444444	0.9571429	0.9428571	0.9714286
13	cfsSMOTE_sig	Yes	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p	1589408941	0.9971039	0.9964570	0.9977508	0.9839587	0.9811215	0.9867678	0.9305556	0.9722222	0.8888889	0.9857143	1.0000000	0.9714286	1589409218	0.9995422	0.9993638	0.9997205	0.9981866	1.0000000	0.9963912	0.9444444	0.9444444	0.9444444	0.9571429	0.9428571	0.9714286
14	fcfsSMOTE	Yes	Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.708.3p + hsa.miR.375.3p + hsa.miR.30e.3p	1589408964	0.9971039	0.9964570	0.9977508	0.9839587	0.9811215	0.9867678	0.9305556	0.9722222	0.8888889	0.9857143	1.0000000	0.9714286	1589409238	0.9995422	0.9993638	0.9997205	0.9981866	1.0000000	0.9963912	0.9444444	0.9444444	0.9444444	0.9571429	0.9428571	0.9714286

Description of columns:

• method - accronym for method
• SMOTE - if balancing using SMOTE or ROSE was used in training dataset.
• miRy - formula used (miRNAs selected).
• *_modelname - the name of .RDS file placed in models/ directory, containing the caret final model that can be used for prediction of new cases. This allows reproducibility of the results. For example glm_ prefix is set according to the method, glm = logistic regression.
• *_train_ROCAUC - area under the ROC curve (AUC ROC) on training dataset, indicating general potential of the model.
• *_train_ROCAUC_lower95CI - lower boundery of 95% confidence interval for AUC ROC.
• *_train_ROCAUC_upper95CI - upper boundery of 95% confidence interval for AUC ROC.
• *_train_Accuracy - accuracy on training set.
• *_train_Sensitivity - sensitivity on training set.
• *_train_Specificity - sensitivity on training set.

By this logic every parameter is also calculated from testing (_test_) and validation (_valid_) set. If the method generated a probability, a default cutoff is used for all of the predictions.

Let’s see the general performance (accuracy) of methods in the benchmark:

metody = OmicSelector_get_benchmark_methods("benchmark.csv")  # gets the methods used in benchmark
par(mfrow = c(2, 2))
for (i in 1:length(metody)) {
    temp = OmicSelector_get_benchmark("benchmark.csv")  # loads benchmark
    temp2 = dplyr::select(temp, starts_with(paste0(metody[i], "_")))
    boxplot(temp[, paste0(metody[i], "_train_Accuracy")], temp[, paste0(metody[i], "_test_Accuracy")], temp[, paste0(metody[i], "_valid_Accuracy")], main = paste0("Method: ", 
        metody[i]), names = c("Training", "Testing", "Validation"), ylab = "Accuracy", ylim = c(0.5, 1))
    tempids = c(match(paste0(metody[i], "_train_Accuracy"), colnames(temp)), match(paste0(metody[i], "_test_Accuracy"), colnames(temp)), match(paste0(metody[i], 
        "_valid_Accuracy"), colnames(temp)))
}
par(mfrow = c(1, 1))

With OmicSelector package, the final optimal feature signature can be selected in 3 ways:

1. Picking the signture which achived the best accuracy in training, testing and validation: (metaindex = mean of all 3 accuracy metrics)

acc1 = OmicSelector_best_signiture_proposals(benchmark_csv = "benchmark.csv", without_train = F)  # generates the benchmark sorted by metaindex
best_signatures = acc1[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])

metaindex	method	miRy
0.9704465	topFCSMOTE	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
0.9666671	cfsSMOTE	Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p
0.9666671	cfsSMOTE_sig	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p

2. Picking the signture which achived the best accuracy in testing and validation: (metaindex = mean of 2 accuracy metrics)

acc1 = OmicSelector_best_signiture_proposals(benchmark_csv = "benchmark.csv", without_train = T)  # generates the benchmark sorted by metaindex
best_signatures = acc1[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])

metaindex	method	miRy
0.9580357	topFC	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
0.9579365	topFCSMOTE	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
0.9544643	cfsSMOTE	Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p

3. The signture which achived the best sensitivity and specificity in validation: (metaindex = mean of sensivitiy and specificity in validation dataset)

acc = OmicSelector_best_signiture_proposals_meta11(benchmark_csv = "benchmark.csv")  # generates the benchmark sorted by metaindex
best_signatures = acc[1:3, ]  # get top 3 methods
OmicSelector_table(best_signatures[, c("metaindex", "method", "miRy")])

metaindex	method	miRy
0.9571429	cfs_sig	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p
0.9571429	topFC	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
0.9428571	topFCSMOTE	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p

It is a good practice to assess learning performance for considered signatures across different classification methods. Here, we visualize the over/underfitting of selected methods by comparing accuracy score between testing and validation sets for 5 top scoring signatures across selection of model architectures.

for (i in 1:length(metody)) {
    suppressMessages(library(PairedData))
    suppressMessages(library(profileR))
    pd = paired(as.numeric(acc[1:5, paste0(metody[i], "_train_Accuracy")]), as.numeric(acc[1:5, paste0(metody[i], "_test_Accuracy")]))
    colnames(pd) = c("Train Acc", "Test Acc")
    plot2 = OmicSelector_profileplot(pd, Method.id = acc$method[1:5], standardize = F)
    pd = paired(as.numeric(acc[1:5, paste0(metody[i], "_train_Accuracy")]), as.numeric(acc[1:5, paste0(metody[i], "_valid_Accuracy")]))
    colnames(pd) = c("Train Acc", "Valid Acc")
    plot3 = OmicSelector_profileplot(pd, Method.id = acc$method[1:5], standardize = F)
    pd = paired(as.numeric(acc[1:5, paste0(metody[i], "_test_Accuracy")]), as.numeric(acc[1:5, paste0(metody[i], "_valid_Accuracy")]))
    colnames(pd) = c("Test Acc", "Valid Acc")
    plot4 = OmicSelector_profileplot(pd, Method.id = acc$method[1:5], standardize = F)
    
    
    
    require(gridExtra)
    grid.arrange(arrangeGrob(plot2, plot3, ncol = 2, nrow = 1, top = metody[i]))
    grid.arrange(arrangeGrob(plot4, ncol = 1, nrow = 1, top = metody[i]))
}

The relationship betweend accuracy on testing and validation sets can also be pictured as scatterplot:

acc2 = acc[1:6, ]  # get top 6 methods
accmelt = melt(acc2, id.vars = "method") %>% filter(variable != "metaindex") %>% filter(variable != "miRy")
accmelt = cbind(accmelt, strsplit2(accmelt$variable, "_"))
acctest = accmelt$value[accmelt$`2` == "test"]
accvalid = accmelt$value[accmelt$`2` == "valid"]
accmeth = accmelt$method[accmelt$`2` == "test"]
unique(accmeth)
#> [1] "cfs_sig"      "topFC"        "topFCSMOTE"   "cfsSMOTE"     "cfsSMOTE_sig"
#> [6] "fcfsSMOTE"
plot5 = ggplot(, aes(x = as.numeric(acctest), y = as.numeric(accvalid), shape = accmeth)) + geom_point() + scale_x_continuous(name = "Accuracy on test set", 
    limits = c(0.5, 1)) + scale_y_continuous(name = "Accuracy on validation set", limits = c(0.5, 1)) + theme_bw()
grid.arrange(arrangeGrob(plot5, ncol = 1, nrow = 1))

7 Best signture analysis

Suppose we decide to use sensitivity and specificity in validation set (e.g. in the model architectures we plan to use in our research) as decisive scoring metric for feature signature. The three best signatures may be:

OmicSelector_table(best_signatures[1:3, 2:4])

method	SMOTE	miRy
cfs_sig	No	Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p
topFC	No	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
topFCSMOTE	Yes	Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p

To get the miRNAs from formula you can use OmicSelector_get_features_from_benchmark.

selected_miRNAs = OmicSelector_get_features_from_benchmark(benchmark_csv = "benchmark.csv", best_signatures$method[1])  # for the best performing signiture
gsub("\\.", "-", selected_miRNAs)  # R doesn't like hyphens, but we can introduce them easly
#>  [1] "hsa-miR-21-5p"    "hsa-miR-30e-3p"   "hsa-miR-30a-3p"   "hsa-miR-30c-2-3p"
#>  [5] "hsa-miR-132-3p"   "hsa-miR-375-3p"   "hsa-miR-217-5p"   "hsa-miR-338-3p"  
#>  [9] "hsa-miR-199b-5p"  "hsa-miR-381-3p"   "hsa-miR-199a-3p"  "hsa-miR-194-5p"  
#> [13] "hsa-miR-134-5p"   "hsa-miR-192-5p"   "hsa-miR-200a-3p"  "hsa-miR-181c-3p" 
#> [17] "hsa-miR-29a-3p"   "hsa-miR-378a-3p"  "hsa-miR-144-5p"   "hsa-miR-335-3p"  
#> [21] "hsa-miR-126-5p"   "hsa-let-7c-5p"    "hsa-miR-378a-5p"  "hsa-miR-181c-5p" 
#> [25] "hsa-miR-126-3p"   "hsa-miR-185-5p"   "hsa-miR-29c-3p"   "hsa-miR-151a-5p" 
#> [29] "hsa-miR-92b-3p"   "hsa-miR-10b-5p"   "hsa-miR-195-5p"   "hsa-miR-101-3p"  
#> [33] "hsa-miR-484"      "hsa-miR-28-3p"

As a double check, we can inspect the differential expression of miRNAs constituating selected signature:

best_de = OmicSelector_best_signiture_de(selected_miRNAs)
OmicSelector_table(best_de)

	miR	log2FC	p-value BH
1	hsa.miR.21.5p	2.6022157	0.0000000
2	hsa.miR.30e.3p	-1.3939819	0.0000000
3	hsa.miR.30a.3p	-2.4419651	0.0000000
4	hsa.miR.30c.2.3p	-2.0824306	0.0000000
5	hsa.miR.132.3p	1.3642193	0.0000000
6	hsa.miR.375.3p	4.7881053	0.0000000
7	hsa.miR.217.5p	4.9968529	0.0000000
10	hsa.miR.338.3p	1.6447027	0.0000000
11	hsa.miR.199b.5p	2.3814574	0.0000000
13	hsa.miR.381.3p	1.6878957	0.0000000
15	hsa.miR.199a.3p	1.2540293	0.0000000
18	hsa.miR.194.5p	2.9439150	0.0000000
19	hsa.miR.134.5p	1.3684465	0.0000000
23	hsa.miR.192.5p	2.9636965	0.0000000
25	hsa.miR.200a.3p	2.1949415	0.0000000
27	hsa.miR.181c.3p	0.9386203	0.0000000
33	hsa.miR.29a.3p	-0.6991346	0.0000000
34	hsa.miR.378a.3p	-1.1444252	0.0000000
39	hsa.miR.144.5p	-2.1127868	0.0000000
41	hsa.miR.335.3p	1.0571023	0.0000000
42	hsa.miR.126.5p	-1.1663511	0.0000000
45	hsa.let.7c.5p	-0.8775535	0.0000000
49	hsa.miR.378a.5p	-1.0287466	0.0000000
57	hsa.miR.181c.5p	0.8614935	0.0000002
58	hsa.miR.126.3p	-0.9851906	0.0000005
61	hsa.miR.185.5p	0.6922687	0.0000020
62	hsa.miR.29c.3p	-0.7856959	0.0000026
65	hsa.miR.151a.5p	0.5057800	0.0000040
73	hsa.miR.92b.3p	0.7783325	0.0000088
77	hsa.miR.10b.5p	-1.2777969	0.0000396
84	hsa.miR.195.5p	-0.7802161	0.0003412
90	hsa.miR.101.3p	-0.5956161	0.0015624
106	hsa.miR.484	-0.3113168	0.0182773
113	hsa.miR.28.3p	-0.2419443	0.0355939

Let’s visualize the performance of those methods using barplots:

for (i in 1:3) {
    cat(paste0("\n\n## ", acc$method[i], "\n\n"))
    par(mfrow = c(1, 2))
    acc = OmicSelector_best_signiture_proposals_meta11("benchmark.csv")
    metody = OmicSelector_get_benchmark_methods("benchmark.csv")
    ktory_set = match(acc$method[i], OmicSelector_get_benchmark("benchmark.csv")$method)
    # do_ktorej_kolumny = which(colnames(acc) == 'metaindex') barplot(as.numeric(acc[i,1:do_ktorej_kolumny]))
    for (ii in 1:length(metody)) {
        
        temp = OmicSelector_get_benchmark("benchmark.csv") %>% dplyr::select(starts_with(paste0(metody[ii], "_t")), starts_with(paste0(metody[ii], "_v")))
        
        ROCtext = paste0("Training AUC ROC: ", round(temp[ktory_set, 1], 2), " (95%CI: ", round(temp[ktory_set, 2], 2), "-", round(temp[ktory_set, 3], 
            2), ")")
        
        temp = temp[, -c(1:3)]
        temp2 = as.numeric(temp[ktory_set, ])
        temp3 = matrix(temp2, nrow = 3, byrow = T)
        colnames(temp3) = c("Accuracy", "Sensitivity", "Specificity")
        rownames(temp3) = c("Training", "Testing", "Validation")
        temp3 = t(temp3)
        
        plot1 = barplot(temp3, beside = T, ylim = c(0, 1), xlab = paste0(ROCtext, "\nBlack - accuracy, blue - sensitivity, green - specificity"), width = 0.85, 
            col = c("black", "blue", "green"), legend = F, args.legend = list(x = "topright", bty = "n", inset = c(0, -0.25)), cex.lab = 0.7, main = paste0(acc$method[i], 
                " - ", metody[ii]), font.lab = 2)
        ## Add text at top of bars
        text(x = plot1, y = as.numeric(temp3), label = paste0(round(as.numeric(temp[ktory_set, ]) * 100, 1), "%"), pos = 3, cex = 0.6, col = "red")
    }
    par(mfrow = c(1, 1))
    
}
#> 
#> 
#> ## cfs_sig

#> 
#> 
#> ## topFC

#> 
#> 
#> ## topFCSMOTE

Finally, we can assess the overlap of top 3 feature selection methods:

overlap = OmicSelector_signiture_overlap(acc$method[1:3], "benchmark.csv")

Which 3 miRNAs are common for all 3 signatures?

attr(overlap, "intersections")[4]
#> $topFC
#> [1] "hsa.miR.708.3p" "hsa.miR.141.3p"

Let’s draw vulcano plot and mark the miRNAs selected in best signature:

OmicSelector_vulcano_plot(selected_miRNAs = de$miR, DE = de, only_label = selected_miRNAs)

Let’s draw heatmap for selected miRNAs in whole dataset (training, testing and validation set).

OmicSelector_heatmap(x = dplyr::select(mixed, gsub("\\.", "-", selected_miRNAs)), rlab = data.frame(Class = mixed$Class, Mix = mixed$mix), zscore = F, margins = c(10, 
    10))

OmicSelector_heatmap(x = dplyr::select(mixed, gsub("\\.", "-", selected_miRNAs)), rlab = data.frame(Class = mixed$Class, Mix = mixed$mix), zscore = T, margins = c(10, 
    10))

Based on everything we have done so far, we suggest using the following signiture in further validation of biomarker study.

cat(paste0(gsub("\\.", "-", selected_miRNAs), collapse = ", "))
#> hsa-miR-21-5p, hsa-miR-30e-3p, hsa-miR-30a-3p, hsa-miR-30c-2-3p, hsa-miR-132-3p, hsa-miR-375-3p, hsa-miR-217-5p, hsa-miR-338-3p, hsa-miR-199b-5p, hsa-miR-381-3p, hsa-miR-199a-3p, hsa-miR-194-5p, hsa-miR-134-5p, hsa-miR-192-5p, hsa-miR-200a-3p, hsa-miR-181c-3p, hsa-miR-29a-3p, hsa-miR-378a-3p, hsa-miR-144-5p, hsa-miR-335-3p, hsa-miR-126-5p, hsa-let-7c-5p, hsa-miR-378a-5p, hsa-miR-181c-5p, hsa-miR-126-3p, hsa-miR-185-5p, hsa-miR-29c-3p, hsa-miR-151a-5p, hsa-miR-92b-3p, hsa-miR-10b-5p, hsa-miR-195-5p, hsa-miR-101-3p, hsa-miR-484, hsa-miR-28-3p

8 Sesssion

session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.2 (2019-12-12)
#>  os       Ubuntu 18.04.4 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       Europe/Warsaw               
#>  date     2020-05-14                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package          * version    date       lib source                       
#>  abind              1.4-5      2016-07-21 [1] CRAN (R 3.6.0)               
#>  arules             1.6-5      2020-04-04 [1] CRAN (R 3.6.2)               
#>  assertthat         0.2.1      2019-03-21 [1] CRAN (R 3.6.0)               
#>  backports          1.1.6      2020-04-05 [1] CRAN (R 3.6.2)               
#>  BiocManager      * 1.30.10    2019-11-16 [1] CRAN (R 3.6.1)               
#>  Biocomb          * 0.4        2018-05-18 [1] CRAN (R 3.6.2)               
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#> 
#> [1] /home/konrad/R/x86_64-pc-linux-gnu-library/3.6
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library

To render this tutorial we used:

render("Tutorial.Rmd", output_file = "Tutorial.html", output_dir = "../static/")

Packages installed in our docker enviorment:

OmicSelector_table(as.data.frame(installed.packages()))

	Package	LibPath	Version	Priority	Depends	Imports	LinkingTo	Suggests	Enhances	License	License_is_FOSS	License_restricts_use	OS_type	MD5sum	NeedsCompilation	Built
abind	abind	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4-5	NA	R (>= 1.5.0)	methods, utils	NA	NA	NA	LGPL (>= 2)	NA	NA	NA	NA	no	3.6.0
acepack	acepack	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.1	NA	NA	NA	NA	testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.0
ada	ada	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0-5	NA	R(>= 2.10),rpart	NA	NA	NA	NA	GPL	NA	NA	NA	NA	no	3.6.1
additivityTests	additivityTests	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-4	NA	NA	NA	NA	knitr	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
ade4	ade4	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.7-15	NA	R (>= 2.10)	graphics, grDevices, methods, stats, utils, MASS, pixmap, sp	NA	ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir, lattice, spdep, splancs, waveslim	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
affy	affy	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.62.0	NA	R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)	affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc	preprocessCore	tkWidgets (>= 1.19.0), affydata, widgetTools	NA	LGPL (>= 2.0)	NA	NA	NA	NA	yes	3.6.1
affyio	affyio	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.54.0	NA	R (>= 2.6.0)	zlibbioc, methods	NA	NA	NA	LGPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
ALL	ALL	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.26.0	NA	R (>= 2.10), Biobase (>= 2.5.5)	NA	NA	rpart	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
amap	amap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.8-18	NA	R (>= 3.6.0)	NA	NA	Biobase	NA	GPL	NA	NA	NA	NA	yes	3.6.1
annotate	annotate	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.62.0	NA	R (>= 2.10), AnnotationDbi (>= 1.27.5), XML	Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), RCurl	NA	hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit,	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.0
AnnotationDbi	AnnotationDbi	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.46.1	NA	R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges	DBI, RSQLite, S4Vectors (>= 0.9.25)	NA	hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
ape	ape	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	5.3	NA	R (>= 3.2.0)	nlme, lattice, graphics, methods, stats, tools, utils, parallel, Rcpp (>= 0.12.0)	Rcpp	gee, expm, igraph	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
apeglm	apeglm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.0	NA	NA	emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp	Rcpp, RcppEigen, RcppNumerical	DESeq2, airway, knitr, rmarkdown, testthat	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
aroma.light	aroma.light	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.14.0	NA	R (>= 2.15.2)	stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.22.0), R.utils (>= 2.7.0), matrixStats (>= 0.54.0)	NA	princurve (>= 2.1.2)	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
arules	arules	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6-5	NA	R (>= 3.4.0), Matrix (>= 1.2-0)	stats, methods, graphics, utils	NA	pmml, XML, arulesViz, testthat	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
arulesViz	arulesViz	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3-3	NA	arules (>= 1.4.1), grid	scatterplot3d, vcd, seriation, igraph (>= 1.0.0), graphics, methods, utils, grDevices, stats, colorspace, DT, plotly, visNetwork	NA	graph, Rgraphviz, iplots, shiny, shinythemes, htmlwidgets	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
askpass	askpass	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1	NA	NA	sys (>= 2.1)	NA	testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.0
assertive	assertive	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3-5	NA	R (>= 3.0.0)	assertive.base (>= 0.0-4), assertive.properties (>= 0.0-2), assertive.types (>= 0.0-2), assertive.numbers, assertive.strings, assertive.datetimes, assertive.files, assertive.sets (>= 0.0-2), assertive.matrices, assertive.models, assertive.data, assertive.data.uk, assertive.data.us, assertive.reflection (>= 0.0-2), assertive.code, knitr	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.base	assertive.base	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-7	NA	R (>= 3.0.0)	methods, utils	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.code	assertive.code	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-3	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2), assertive.properties, assertive.types, methods	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.data	assertive.data	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-3	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2), assertive.strings	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.data.uk	assertive.data.uk	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-2	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2), assertive.strings	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.data.us	assertive.data.us	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-2	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2), assertive.strings	NA	testthat, devtools	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.datetimes	assertive.datetimes	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-2	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2), assertive.types	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.files	assertive.files	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-2	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2), assertive.numbers	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.matrices	assertive.matrices	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-2	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2)	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.models	assertive.models	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-2	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2), stats	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.numbers	assertive.numbers	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-2	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2)	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.properties	assertive.properties	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-4	NA	R (>= 3.0.0)	assertive.base (>= 0.0-7), methods	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.reflection	assertive.reflection	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-4	NA	R (>= 3.0.0)	assertive.base (>= 0.0-7), utils	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.sets	assertive.sets	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-3	NA	R (>= 3.0.0)	assertive.base (>= 0.0-7)	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.strings	assertive.strings	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-3	NA	R (>= 3.0.0)	assertive.base (>= 0.0-2), assertive.types, stringi	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertive.types	assertive.types	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-3	NA	R (>= 3.0.0)	assertive.base (>= 0.0-7), assertive.properties, codetools, methods, stats	NA	testthat, data.table, dplyr, xml2	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
assertthat	assertthat	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.1	NA	NA	tools	NA	testthat, covr	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
backports	backports	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.6	NA	R (>= 3.0.0)	utils	NA	NA	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
bartMachine	bartMachine	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.4.2	NA	R (>= 2.14.0), rJava (>= 0.9-8), bartMachineJARs (>= 1.0), car, randomForest, missForest	graphics, grDevices, stats	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
bartMachineJARs	bartMachineJARs	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1	NA	R (>= 2.14.0), rJava (>= 0.9-8)	NA	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
base64enc	base64enc	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-3	NA	R (>= 2.9.0)	NA	NA	NA	png	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.0
BBmisc	BBmisc	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.11	NA	NA	utils, methods, stats, checkmate (>= 1.8.0)	NA	testthat, microbenchmark, codetools	NA	BSD_2_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.1
bbmle	bbmle	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.23.1	NA	R (>= 3.0.0), stats4	stats, numDeriv, lattice, MASS, methods, bdsmatrix, Matrix, mvtnorm	NA	emdbook, rms, ggplot2, RUnit, MuMIn, AICcmodavg, Hmisc, optimx (>= 2013.8.6), knitr, testthat	NA	GPL	NA	NA	NA	NA	no	3.6.2
bdsmatrix	bdsmatrix	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3-4	NA	methods, R (>= 2.0.0)	NA	NA	NA	NA	LGPL-2	NA	NA	NA	NA	yes	3.6.1
beachmat	beachmat	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.0	NA	NA	methods, DelayedArray, BiocGenerics	NA	testthat, BiocStyle, knitr, rmarkdown, Matrix, devtools	NA	GPL-3	NA	NA	NA	NA	yes	3.6.0
beeswarm	beeswarm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.3	NA	NA	stats, graphics, grDevices, utils	NA	NA	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.0
bench	bench	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.1	NA	R (>= 3.1)	glue, methods, pillar, profmem, rlang (>= 0.2.0), stats, tibble, utils	NA	covr, dplyr, forcats, ggbeeswarm, ggplot2, ggridges, mockery, parallel, scales, testthat, tidyr (>= 0.8.1), vctrs, withr	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
bestNormalize	bestNormalize	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5.0	NA	R (>= 3.1.0)	LambertW, nortest, dplyr, doParallel, foreach, doRNG, recipes, tibble	NA	knitr, rmarkdown, MASS, testthat, mgcv, parallel	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
BGLR	BGLR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.8	NA	R (>= 3.5.0)	truncnorm	NA	NA	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
BH	BH	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.72.0-3	NA	NA	NA	NA	NA	NA	BSL-1.0	NA	NA	NA	NA	no	3.6.1
bibtex	bibtex	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4.2.2	NA	R (>= 3.0.2)	stringr, utils	NA	testthat	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
biclust	biclust	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.2	NA	R (>= 2.10), MASS, grid, colorspace, lattice	methods, flexclust, additivityTests, tidyr, ggplot2	NA	isa2	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
Biobase	Biobase	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.44.0	NA	R (>= 2.10), BiocGenerics (>= 0.27.1), utils	methods	NA	tools, tkWidgets, ALL, RUnit, golubEsets	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.0
BiocGenerics	BiocGenerics	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.30.0	NA	R (>= 3.6.0), methods, utils, graphics, stats, parallel	methods, utils, graphics, stats, parallel	NA	Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.0
BiocManager	BiocManager	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.30.10	NA	NA	utils	NA	BiocStyle, BiocVersion, remotes, testthat, withr, curl, knitr	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
BiocNeighbors	BiocNeighbors	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.0	NA	NA	Rcpp, BiocGenerics, S4Vectors, BiocParallel, stats, methods	Rcpp, RcppAnnoy, RcppHNSW	testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW	NA	GPL-3	NA	NA	NA	NA	yes	3.6.0
Biocomb	Biocomb	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4	NA	R (>= 2.13.0),gtools,Rcpp (>= 0.12.1)	rgl, MASS, e1071, randomForest, pROC, ROCR, arules, pamr, class, nnet, rpart, FSelector, RWeka, grDevices, graphics, stats, utils	Rcpp	NA	NA	GPL (>= 3)	NA	NA	NA	NA	yes	3.6.2
BiocParallel	BiocParallel	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.18.1	NA	methods	stats, utils, futile.logger, parallel, snow	BH	BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
BiocSingular	BiocSingular	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	NA	BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, irlba, rsvd, Rcpp	Rcpp, beachmat	testthat, BiocStyle, knitr, rmarkdown, beachmat	NA	GPL-3	NA	NA	NA	NA	yes	3.6.0
BiocStyle	BiocStyle	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.12.0	NA	NA	bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager	NA	BiocGenerics, RUnit, htmltools	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.2
BiocVersion	BiocVersion	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.9.0	NA	R (>= 3.6.0), R (< 3.7.0)	NA	NA	NA	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.0
biomaRt	biomaRt	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.40.5	NA	methods	utils, XML, RCurl, AnnotationDbi, progress, stringr, httr	NA	annotate, BiocStyle, knitr, rmarkdown, testthat	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
biostatUZH	biostatUZH	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.8.0	NA	R (>= 2.15.0), grDevices, graphics, stats, survival (>= 2.35)	boot	NA	cmprsk, lme4, prodlim, psy, xtable, reporttools, Hmisc, surveillance, carData	MASS, ellipse	GPL (>=2)	NA	NA	NA	NA	no	3.6.2
Biostrings	Biostrings	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.52.0	NA	R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13), IRanges, XVector (>= 0.23.2)	graphics, methods, stats, utils	S4Vectors, IRanges, XVector	BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit	Rmpi	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
bit	bit	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-15.2	NA	R (>= 2.9.2)	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
bit64	bit64	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9-7	NA	R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.0
bitops	bitops	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-6	NA	NA	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.0
blob	blob	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.1	NA	NA	methods, rlang, vctrs (>= 0.2.1)	NA	covr, crayon, pillar (>= 1.2.1), testthat	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
bmp	bmp	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3	NA	NA	NA	NA	pixmap, testthat	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
bookdown	bookdown	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.18	NA	NA	htmltools (>= 0.3.6), knitr (>= 1.22), rmarkdown (>= 2.0), xfun (>= 0.6), tinytex (>= 0.12)	NA	htmlwidgets, rstudioapi, miniUI, rsconnect (>= 0.4.3), servr (>= 0.13), shiny, testit (>= 0.9), tufte, webshot	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
bootstrap	bootstrap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2019.6	NA	stats, R (>= 2.10.0)	NA	NA	NA	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.0
Boruta	Boruta	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	6.0.0	NA	ranger	NA	NA	mlbench, rFerns, randomForest, testthat, xgboost	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
bounceR	bounceR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1	NA	R (>= 3.4.3)	purrr, furrr, parallel, mboost, strucchange, np, reshape2, ggplot2, mRMRe, dplyr, future	NA	NA	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
BradleyTerry2	BradleyTerry2	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-2	NA	R (>= 2.10)	brglm, gtools, lme4 (>= 1.0), qvcalc, stats	NA	prefmod, testthat	gnm	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
brew	brew	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-6	NA	NA	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	NA	3.6.1
brglm	brglm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.2	NA	R (>= 2.6.0), profileModel	NA	NA	MASS	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
broom	broom	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.6	NA	R (>= 3.1)	backports, dplyr, generics (>= 0.0.2), methods, nlme, purrr, reshape2, stringr, tibble (>= 3.0.0), tidyr	NA	AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot, brms, btergm, car, caret, coda, covr, e1071, emmeans, ergm, gam (>= 1.15), gamlss, gamlss.data, gamlss.dist, geepack, ggplot2, glmnet, gmm, Hmisc, irlba, Kendall, knitr, ks, Lahman, lavaan, lfe, lme4, lmodel2, lmtest, lsmeans, maps, maptools, MASS, Matrix, mclust, mgcv, muhaz, multcomp, network, nnet, orcutt (>= 2.2), ordinal, plm, plyr, poLCA, psych, quantreg, rgeos, rmarkdown, rsample, rstan, rstanarm, sp, speedglm, statnet.common, survey, survival, testthat, tseries, zoo	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
C50	C50	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.3	NA	R (>= 2.10.0)	partykit, Cubist (>= 0.2.3)	NA	knitr, modeldata	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
ca	ca	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.71.1	NA	R (>= 3.0.0)	NA	NA	rgl (>= 0.64-10), vcd	NA	GPL	NA	NA	NA	NA	no	3.6.2
Cairo	Cairo	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5-12	NA	R (>= 2.4.0)	grDevices, graphics	NA	png	FastRWeb	GPL-2	NA	NA	NA	NA	yes	3.6.2
calibrate	calibrate	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.7.5	NA	R (>= 3.5.0), MASS	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
callr	callr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.4.3	NA	NA	processx (>= 3.4.0), R6, utils	NA	cliapp, covr, crayon, fansi, pingr, ps, rprojroot, spelling, testthat, tibble, withr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
car	car	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.0-7	NA	R (>= 3.5.0), carData (>= 3.0-0)	abind, MASS, mgcv, nnet, pbkrtest (>= 0.4-4), quantreg, grDevices, utils, stats, graphics, maptools, rio, lme4, nlme	NA	alr4, boot, coxme, knitr, leaps, lmtest, Matrix, MatrixModels, rgl (>= 0.93.960), sandwich, SparseM, survival, survey	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
carData	carData	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.0-3	NA	R (>= 3.0)	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
caret	caret	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	6.0-86	NA	R (>= 3.2.0), lattice (>= 0.20), ggplot2	foreach, methods, plyr, ModelMetrics (>= 1.2.2.2), nlme, reshape2, stats, stats4, utils, grDevices, recipes (>= 0.1.10), withr (>= 2.0.0), pROC,	NA	BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam (>= 1.15), ipred, kernlab, knitr, klaR, MASS, ellipse, mda, mgcv, mlbench, MLmetrics, nnet, party (>= 0.9-99992), pls, proxy, randomForest, RANN, spls, subselect, pamr, superpc, Cubist, testthat (>= 0.9.1), rpart, dplyr, covr	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
caretEnsemble	caretEnsemble	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.1	NA	R (>= 3.2.0)	methods, pbapply, ggplot2, digest, plyr, lattice, gridExtra, data.table, caret	NA	caTools, testthat, lintr, randomForest, glmnet, rpart, kernlab, nnet, e1071, ipred, pROC, knitr, mlbench, MASS, gbm, klaR, rmarkdown	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
caTools	caTools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.18.0	NA	R (>= 3.6.0)	bitops	NA	MASS, rpart	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
cba	cba	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2-21	NA	R (>= 2.10), grid, proxy	stats, graphics, grDevices, methods	NA	gclus, colorspace	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
cellranger	cellranger	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	R (>= 3.0.0)	rematch, tibble	NA	covr, testthat (>= 1.0.0), knitr, rmarkdown	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
CGEN	CGEN	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.20.0	NA	R (>= 2.10.1), survival, mvtnorm	NA	NA	cluster	NA	GPL-2 + file LICENSE	NA	NA	NA	NA	yes	3.6.0
checkmate	checkmate	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.0	NA	R (>= 3.0.0)	backports (>= 1.1.0), utils	NA	R6, fastmatch, data.table (>= 1.9.8), devtools, ggplot2, knitr, magrittr, microbenchmark, rmarkdown, testthat (>= 0.11.0), tinytest (>= 1.1.0), tibble	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
chron	chron	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3-55	NA	R (>= 2.12.0)	graphics, stats	NA	scales, ggplot2	zoo	GPL-2	NA	NA	NA	NA	yes	3.6.2
circlize	circlize	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4.9	NA	R (>= 3.0.0), graphics	GlobalOptions (>= 0.1.0), shape, grDevices, utils, stats, colorspace, methods, grid	NA	knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 2.0.0), gridBase, png	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
CircStats	CircStats	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2-6	NA	MASS, boot	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
classInt	classInt	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-3	NA	R (>= 2.2)	grDevices, stats, graphics, e1071, class, KernSmooth	NA	spData (>= 0.2.6.2), units, knitr, rmarkdown	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
cli	cli	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.2	NA	R (>= 2.10)	assertthat, crayon (>= 1.3.4), glue, methods, utils, fansi	NA	callr, covr, htmlwidgets, knitr, mockery, rmarkdown, rstudioapi, prettycode (>= 1.1.0), testthat, withr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
clipr	clipr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.7.0	NA	NA	utils	NA	covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>= 2.0.0)	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
clisymbols	clisymbols	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.0	NA	NA	NA	NA	testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
clue	clue	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3-57	NA	R (>= 3.2.0)	stats, cluster, graphics, methods	NA	e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations	RWeka, ape, cba, cclust, flexclust, flexmix, kernlab, mclust, movMF, modeltools	GPL-2	NA	NA	NA	NA	yes	3.6.1
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clusterProfiler	clusterProfiler	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.12.0	NA	R (>= 3.4.0)	AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7), ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rvcheck, stats, tidyr, utils	NA	AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
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cmprsk	cmprsk	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.2-9	NA	R (>= 3.0.0), survival	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
coda	coda	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.19-3	NA	R (>= 2.14.0)	lattice	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
coin	coin	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3-1	NA	R (>= 3.4.0), survival	methods, parallel, stats, stats4, utils, libcoin (>= 1.0-0), matrixStats (>= 0.54.0), modeltools (>= 0.2-9), mvtnorm (>= 1.0-5), multcomp	libcoin (>= 1.0-0)	xtable, e1071, vcd, TH.data (>= 1.0-7)	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
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combinat	combinat	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-8	NA	NA	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	NA	3.6.0
commonmark	commonmark	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.7	NA	NA	NA	NA	curl, testthat, xml2	NA	BSD_2_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.1
compare	compare	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2-6	NA	NA	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
ComplexHeatmap	ComplexHeatmap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.0	NA	R (>= 3.1.2), methods, grid, graphics, stats, grDevices	circlize (>= 0.4.5), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png	NA	testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
config	config	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3	NA	NA	yaml (>= 2.1.13)	NA	testthat, knitr	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
ConsensusClusterPlus	ConsensusClusterPlus	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.48.0	NA	NA	Biobase, ALL, graphics, stats, utils, cluster	NA	NA	NA	GPL version 2	NA	NA	NA	NA	no	3.6.1
corpcor	corpcor	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.9	NA	R (>= 3.0.2)	stats	NA		NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
corrplot	corrplot	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.84	NA	NA	NA	NA	knitr, RColorBrewer, testthat	NA	GPL	NA	NA	NA	NA	no	3.6.1
covr	covr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.5.0	NA	R (>= 3.1.0), methods	digest, stats, utils, jsonlite, rex, httr, crayon, withr (>= 1.0.2), yaml	NA	R6, knitr, rmarkdown, htmltools, DT (>= 0.2), testthat, rlang, rstudioapi (>= 0.2), xml2 (>= 1.0.0), parallel, memoise, mockery	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
cowplot	cowplot	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	R (>= 3.5.0)	ggplot2 (> 2.2.1), grid, gtable, grDevices, methods, rlang, scales, utils	NA	Cairo, covr, dplyr, forcats, gridGraphics (>= 0.4-0), knitr, lattice, magick, maps, PASWR, rmarkdown, testthat (>= 1.0.0), tidyr, vdiffr (>= 0.3.0), VennDiagram	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
cqn	cqn	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.30.0	NA	R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg	splines	NA	scales, edgeR	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
cr17	cr17	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.0	NA	ggplot2 (>= 2.2.1), survival (>= 2.41-3), cmprsk (>= 2.2-7), gridExtra (>= 2.2.1), R (>= 3.3.2)	dplyr (>= 0.5.0), scales (>= 0.4.1), grid (>= 3.3.0), gtable (>= 0.2.0)	NA	knitr, rmarkdown	NA	GPL	NA	NA	NA	NA	no	3.6.2
crayon	crayon	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.4	NA	NA	grDevices, methods, utils	NA	mockery, rstudioapi, testthat, withr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
crosstalk	crosstalk	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0.1	NA	NA	htmltools (>= 0.3.6), jsonlite, lazyeval, R6	NA	shiny, ggplot2, testthat (>= 2.1.0)	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
crrstep	crrstep	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2015-2.1	NA	cmprsk	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
crul	crul	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9.0	NA	NA	curl (>= 3.3), R6 (>= 2.2.0), urltools (>= 1.6.0), httpcode (>= 0.2.0), jsonlite, mime	NA	testthat, fauxpas (>= 0.1.0), webmockr (>= 0.1.0), knitr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
cubature	cubature	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.4	NA	NA	Rcpp	Rcpp	testthat, knitr, mvtnorm, benchr	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
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curl	curl	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	4.3	NA	R (>= 3.0.0)	NA	NA	spelling, testthat (>= 1.0.0), knitr, jsonlite, rmarkdown, magrittr, httpuv (>= 1.4.4), webutils	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.1
cutpointr	cutpointr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.2	NA	R (>= 3.5.0)	gridExtra (>= 2.2.1), foreach (>= 1.4.3), dplyr (>= 0.8.0), tidyr (>= 1.0.0), purrr (>= 0.3.0), tibble (>= 3.0.0), ggplot2 (>= 3.0.0), Rcpp (>= 0.12.12), stats, utils, rlang (>= 0.4.0)	Rcpp	KernSmooth (>= 2.23-15), fANCOVA (>= 0.5-1), testthat (>= 1.0.2), doRNG (>= 1.6), doParallel (>= 1.0.11), knitr, rmarkdown, mgcv (>= 1.8), crayon (>= 1.3.4), registry (>= 0.5-1), pkgmaker(>= 0.31.1),	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
cyclocomp	cyclocomp	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	NA	callr, crayon, desc, remotes, withr	NA	testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
d3heatmap	d3heatmap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.1.2	NA	NA	scales (>= 0.2.5), htmlwidgets, png, base64enc, dendextend (>= 0.18.0), stats, grDevices	NA	shiny, knitr, rmarkdown	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	no	3.6.1
data.table	data.table	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.12.8	NA	R (>= 3.1.0)	methods	NA	bit64, curl, R.utils, knitr, xts, nanotime, zoo, yaml	NA	MPL-2.0 | file LICENSE	NA	NA	NA	NA	yes	3.6.2
DBI	DBI	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	methods, R (>= 3.0.0)	NA	NA	blob, covr, hms, knitr, magrittr, rmarkdown, rprojroot, RSQLite (>= 1.1-2), testthat, xml2	NA	LGPL (>= 2.1)	NA	NA	NA	NA	no	3.6.1
dbplyr	dbplyr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.3	NA	R (>= 3.1)	assertthat (>= 0.2.0), DBI (>= 1.0.0), dplyr (>= 0.8.0), glue (>= 1.2.0), lifecycle, methods, purrr (>= 0.2.5), R6 (>= 2.2.2), rlang (>= 0.2.0), tibble (>= 1.4.2), tidyselect (>= 0.2.4), utils	NA	bit64, covr, knitr, Lahman, nycflights13, RMariaDB (>= 1.0.2), rmarkdown, RPostgres (>= 1.1.3), RSQLite (>= 2.1.0), testthat (>= 2.0.0)	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
dbscan	dbscan	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-5	NA	NA	Rcpp (>= 1.0.0), graphics, stats, methods	Rcpp	fpc, microbenchmark, testthat, dendextend, igraph, knitr, DMwR	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
deepnet	deepnet	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2	NA	NA	NA	NA	NA	NA	GPL	NA	NA	NA	NA	no	3.6.2
DelayedArray	DelayedArray	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.10.0	NA	R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.27.1), S4Vectors (>= 0.21.7), IRanges (>= 2.17.3), BiocParallel	stats, Matrix	S4Vectors	Matrix, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.0
DelayedMatrixStats	DelayedMatrixStats	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.1	NA	DelayedArray (>= 0.9.8)	methods, matrixStats (>= 0.55.0), Matrix, S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.7.10), BiocParallel	NA	testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
dendextend	dendextend	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.13.4	NA	R (>= 3.0.0)	utils, stats, datasets, magrittr (>= 1.0.1), ggplot2, viridis	NA	knitr, rmarkdown, testthat, seriation, colorspace, ape, microbenchmark, gplots, heatmaply, d3heatmap, dynamicTreeCut, pvclust, corrplot, DendSer, MASS, cluster, fpc, circlize (>= 0.2.5), covr	ggdendro, dendroextras, Hmisc, data.table, rpart	GPL-2 | GPL-3	NA	NA	NA	NA	no	3.6.2
DendSer	DendSer	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.1	NA	gclus,seriation	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
DEoptimR	DEoptimR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-8	NA	NA	stats	NA	NA	robustbase	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
Deriv	Deriv	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	4.0	NA	NA	methods	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
desc	desc	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.0	NA	R (>= 3.1.0)	assertthat, utils, R6, crayon, rprojroot	NA	covr, testthat, whoami, withr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
descr	descr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.4	NA	NA	xtable, utils, grDevices, graphics, stats	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
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DESeq2	DESeq2	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.24.0	NA	S4Vectors (>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6)	BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0)	Rcpp, RcppArmadillo	testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10)	NA	LGPL (>= 3)	NA	NA	NA	NA	yes	3.6.0
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devtools	devtools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3.0	NA	R (>= 3.0.2), usethis (>= 1.6.0)	callr (>= 3.4.3), cli (>= 2.0.2), covr (>= 3.5.0), crayon (>= 1.3.4), desc (>= 1.2.0), digest (>= 0.6.25), DT (>= 0.13), ellipsis (>= 0.3.0), glue (>= 1.4.0), git2r (>= 0.26.1), httr (>= 1.4.1), jsonlite (>= 1.6.1), memoise (>= 1.1.0), pkgbuild (>= 1.0.6), pkgload (>= 1.0.2), rcmdcheck (>= 1.3.3), remotes (>= 2.1.1), rlang (>= 0.4.5), roxygen2 (>= 7.1.0), rstudioapi (>= 0.11), rversions (>= 2.0.1), sessioninfo (>= 1.1.1), stats, testthat (>= 2.3.2), tools, utils, withr (>= 2.1.2)	NA	BiocManager (>= 1.30.10), curl (>= 4.3), foghorn (>= 1.1.5), gmailr (>= 1.0.0), knitr (>= 1.28), lintr (>= 2.0.1), mockery (>= 0.4.2), pingr (>= 2.0.0), MASS, pkgdown (>= 1.5.1), rhub (>= 1.1.1), rmarkdown (>= 2.1), spelling (>= 2.1)	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
DiagrammeR	DiagrammeR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.6.1	NA	R (>= 3.2.0)	dplyr (>= 0.7.6), downloader (>= 0.4), glue (>= 1.3.0), htmltools (>= 0.3.6), htmlwidgets (>= 1.2), igraph (>= 1.2.2), influenceR (>= 0.1.0), magrittr (>= 1.5), purrr (>= 0.2.5), RColorBrewer (>= 1.1-2), readr (>= 1.1.1), rlang (>= 0.2.2), rstudioapi (>= 0.7), scales (>= 1.0.0), stringr (>= 1.3.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), viridis (>= 0.5.1), visNetwork (>= 2.0.4)	NA	covr, DiagrammeRsvg, rsvg, knitr, testthat, rmarkdown	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
diffobj	diffobj	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	R (>= 3.1.0)	crayon (>= 1.3.2), tools, methods, utils, stats	NA	knitr, rmarkdown, testthat	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
digest	digest	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.25	NA	R (>= 3.1.0)	utils	NA	tinytest, knitr, rmarkdown	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
diptest	diptest	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.75-7	NA	NA	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
DMwR	DMwR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4.1	NA	R(>= 2.10), methods, graphics, lattice (>= 0.18-3), grid (>= 2.10.1)	xts (>= 0.6-7), quantmod (>= 0.3-8), zoo (>= 1.6-4), abind (>= 1.1-0), rpart (>= 3.1-46), class (>= 7.3-1), ROCR (>= 1.0)	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
DO.db	DO.db	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.9	NA	R (>= 2.7.0), methods, AnnotationDbi (>= 1.9.7)	methods, AnnotationDbi	NA	NA	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
doBy	doBy	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	4.6.5	NA	R (>= 3.6.0), methods	pbkrtest (>= 0.4-8.1), MASS, Matrix, dplyr, plyr, magrittr, Deriv, tibble, broom	NA	multcomp, geepack, lme4, survival, ggplot2, knitr	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
docker4seq	docker4seq	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3.4	NA	R (>= 3.0.0)	NA	NA	BiocStyle, knitr, rmarkdown	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
doParallel	doParallel	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.15	NA	R (>= 2.14.0), foreach(>= 1.2.0), iterators(>= 1.0.0), parallel, utils	NA	NA	caret, mlbench, rpart, RUnit	compiler	GPL-2	NA	NA	NA	NA	no	3.6.2
doRNG	doRNG	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.8.2	NA	R (>= 3.0.0), foreach, rngtools (>= 1.5)	stats, utils, iterators	NA	doParallel, doMPI, doRedis, rbenchmark, devtools, knitr, bibtex, testthat, pkgmaker (>= 0.31)	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
DOSE	DOSE	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.10.2	NA	R (>= 3.4.0)	AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim (>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils	NA	prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
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dotCall64	dotCall64	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-0	NA	R (>= 3.1)	NA	NA	microbenchmark, OpenMPController, RColorBrewer, roxygen2, spam, testthat,	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
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dplyr	dplyr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.8.5	NA	R (>= 3.2.0)	ellipsis, assertthat (>= 0.2.0), glue (>= 1.3.0), magrittr (>= 1.5), methods, pkgconfig, R6, Rcpp (>= 1.0.1), rlang (>= 0.4.0), tibble (>= 2.0.0), tidyselect (>= 0.2.5), utils	BH, plogr (>= 0.2.0), Rcpp (>= 1.0.1)	bit64, callr, covr, crayon (>= 1.3.4), DBI, dbplyr, dtplyr, ggplot2, hms, knitr, Lahman, lubridate, MASS, mgcv, microbenchmark, nycflights13, rmarkdown, RMySQL, RPostgreSQL, RSQLite, testthat, withr, broom, purrr, readr	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
DT	DT	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.13	NA	NA	htmltools (>= 0.3.6), htmlwidgets (>= 1.3), jsonlite (>= 0.9.16), magrittr, crosstalk, promises	NA	knitr (>= 1.8), rmarkdown, shiny (>= 1.2.0)	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	no	3.6.2
dtplyr	dtplyr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.1	NA	R (>= 3.2)	crayon, data.table (>= 1.12.4), dplyr (>= 0.8.1), rlang, tibble, tidyselect	NA	bench, covr, knitr, rmarkdown, testthat (>= 2.1.0)	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
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e1071	e1071	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.7-3	NA	NA	graphics, grDevices, class, stats, methods, utils	NA	cluster, mlbench, nnet, randomForest, rpart, SparseM, xtable, Matrix, MASS, slam	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
earth	earth	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	5.1.2	NA	R (>= 3.4.0), Formula (>= 1.2-3), plotmo (>= 3.5.4), TeachingDemos (>= 2.10)	NA	NA	gam (>= 1.16), mgcv (>= 1.8-26), mda (>= 0.4-10), MASS (>= 7.3-51)	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
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emdbook	emdbook	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.12	NA	NA	MASS, lattice, plyr, coda, bbmle	NA	R2jags, ellipse, SuppDists, numDeriv, testthat, rgl	NA	GPL	NA	NA	NA	NA	no	3.6.2
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enrichplot	enrichplot	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.0	NA	R (>= 3.4.0)	AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2, ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices, grid, gridExtra, igraph, methods, purrr, RColorBrewer, reshape2, stats, UpSetR, utils	NA	clusterProfiler, dplyr, knitr, org.Hs.eg.db, prettydoc	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
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exactRankTests	exactRankTests	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.8-31	NA	R (>= 2.4.0), stats, utils	NA	NA	survival	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
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funModeling	funModeling	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.9.3	NA	R (>= 3.4.0), Hmisc (>= 3.17.1)	ROCR, ggplot2, gridExtra, pander, reshape2, scales, dplyr, lazyeval, utils, RColorBrewer, moments, entropy, cli, stringr	NA	knitr, rmarkdown	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
furrr	furrr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.0	NA	R (>= 3.2.0), future (>= 1.6.2)	globals (>= 0.10.3), rlang (>= 0.2.0), purrr (>= 0.2.4)	NA	listenv (>= 0.6.0), dplyr (>= 0.7.4), testthat	NA	LGPL (>= 2.1)	NA	NA	NA	NA	no	3.6.1
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future	future	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.17.0	NA	NA	digest, globals (>= 0.12.5), listenv (>= 0.8.0), parallel, utils	NA	RhpcBLASctl, R.rsp, markdown	NA	LGPL (>= 2.1)	NA	NA	NA	NA	no	3.6.2
GA	GA	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.2.1	NA	R (>= 3.4), methods, foreach, iterators	stats, graphics, grDevices, utils, cli, crayon, Rcpp	Rcpp, RcppArmadillo	parallel, doParallel, doRNG (>= 1.6), knitr (>= 1.8)	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
gam	gam	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.16.1	NA	stats, splines, foreach	NA	NA	akima	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
gargle	gargle	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.0	NA	R (>= 3.2)	fs (>= 1.3.1), glue (>= 1.3.0), httr (>= 1.4.0), jsonlite, rlang (>= 0.4.2), stats, withr	NA	covr, knitr, rmarkdown, sodium, spelling, testthat (>= 2.3.2)	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
gbm	gbm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1.5	NA	R (>= 2.9.0)	gridExtra, lattice, parallel, survival	NA	knitr, pdp, RUnit, splines, viridis	NA	GPL (>= 2) | file LICENSE	NA	NA	NA	NA	yes	3.6.0
gclus	gclus	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.2	NA	R (>= 2.10), cluster	NA	NA	knitr, rmarkdown	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
gdata	gdata	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.18.0	NA	R (>= 2.3.0)	gtools, stats, methods, utils	NA	RUnit	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
GDCRNATools	GDCRNATools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.1	NA	R (>= 3.5.0)	shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel	NA	knitr, testthat	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.2
gdtools	gdtools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.2	NA	NA	Rcpp (>= 0.12.12), systemfonts (>= 0.1.1)	Rcpp	htmltools, testthat, fontquiver (>= 0.2.0), curl	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	yes	3.6.2
geepack	geepack	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3-1	NA	R (>= 3.5.0), methods	MASS, broom, magrittr	NA	NA	NA	GPL (>= 3)	NA	NA	NA	NA	yes	3.6.1
genefilter	genefilter	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.66.0	NA	NA	S4Vectors (>= 0.9.42), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival	NA	class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.0
geneplotter	geneplotter	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.62.0	NA	R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate	AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils	NA	Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.0
generics	generics	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0.2	NA	R (>= 3.1)	methods	NA	covr, pkgload, testthat, tibble	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
genetics	genetics	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.8.1.2	NA	combinat, gdata, gtools, MASS, mvtnorm	NA	NA	NA	NA	GPL	NA	NA	NA	NA	no	3.6.0
GenomeInfoDb	GenomeInfoDb	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.20.0	NA	R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12)	stats, stats4, utils, RCurl, GenomeInfoDbData	NA	GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.0
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GenomicRanges	GenomicRanges	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.36.1	NA	R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.19.11), IRanges (>= 2.17.1), GenomeInfoDb (>= 1.15.2)	utils, stats, XVector (>= 0.19.8)	S4Vectors, IRanges	Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
GetoptLong	GetoptLong	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.8	NA	R (>= 3.0.0)	rjson, GlobalOptions (>= 0.1.0), methods	NA	testthat (>= 1.0.0), knitr, markdown	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
GGally	GGally	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5.0	NA	R (>= 3.1), ggplot2 (> 2.2.0)	grDevices, grid, gtable (>= 0.2.0), plyr (>= 1.8.3), progress, RColorBrewer, reshape (>= 0.8.5), utils, rlang	NA	broom (>= 0.4.0), chemometrics, geosphere (>= 1.5-1), igraph (>= 1.0.1), intergraph (>= 2.0-2), maps (>= 3.1.0), mapproj, network (>= 1.12.0), scagnostics, scales (>= 0.4.0), sna (>= 2.3-2), survival, packagedocs (>= 0.4.0), rmarkdown, roxygen2, testthat, crosstalk	NA	GPL (>= 2.0)	NA	NA	NA	NA	no	3.6.2
ggbeeswarm	ggbeeswarm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.0	NA	R (>= 3.0.0), ggplot2 (>= 2.0)	beeswarm, vipor	NA	gridExtra	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.0
ggbiplot	ggbiplot	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.55	NA	ggplot2, plyr, scales, grid	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
ggdendro	ggdendro	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-20	NA	NA	MASS, ggplot2(>= 0.9.2)	NA	rpart(>= 4.0-0), tree, testthat, knitr, cluster, scales	NA	GPL-2 | GPL-3	NA	NA	NA	NA	no	3.6.1
ggforce	ggforce	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.1	NA	ggplot2 (>= 3.0.0), R (>= 3.3.0)	Rcpp (>= 0.12.2), grid, scales, MASS, tweenr (>= 0.1.5), gtable, rlang, polyclip, stats, grDevices, tidyselect, withr, utils	Rcpp, RcppEigen	sessioninfo, concaveman, deldir, reshape2, units (>= 0.4-6)	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.1
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ggplotify	ggplotify	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0.5	NA	R (>= 3.4.0)	ggplot2, graphics, grDevices, grid, gridGraphics, rvcheck	NA	colorspace, cowplot, ggimage, knitr, lattice, prettydoc, vcd	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.2
ggpubr	ggpubr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	R (>= 3.1.0), ggplot2	ggrepel, grid, ggsci, stats, utils, tidyr, purrr, dplyr (>= 0.7.1), cowplot, ggsignif, scales, gridExtra, glue, polynom, rlang, rstatix (>= 0.4.0), tibble, magrittr	NA	grDevices, knitr, RColorBrewer, gtable	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
ggraph	ggraph	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.2	NA	R (>= 2.10), ggplot2 (>= 3.0.0)	Rcpp (>= 0.12.2), dplyr, ggforce (>= 0.3.1), grid, igraph (>= 1.0.0), scales, MASS, digest, gtable, ggrepel, utils, stats, viridis, rlang, tidygraph, graphlayouts (>= 0.5.0)	Rcpp	network, knitr, rmarkdown, purrr, tibble, seriation, deldir, gganimate	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
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ggrepel	ggrepel	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.8.2	NA	R (>= 3.0.0), ggplot2 (>= 2.2.0)	grid, Rcpp, scales (>= 0.3.0)	Rcpp	knitr, rmarkdown, testthat, gridExtra, devtools, prettydoc	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	yes	3.6.2
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ggsci	ggsci	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.9	NA	R (>= 3.0.2)	grDevices, scales, ggplot2 (>= 2.0.0)	NA	knitr, rmarkdown, gridExtra, reshape2	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	no	3.6.0
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git2r	git2r	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.27.1	NA	R (>= 3.1)	graphics, utils	NA	getPass	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
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glmnet	glmnet	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.0-2	NA	R (>= 3.6.0), Matrix (>= 1.0-6)	methods, utils, foreach, shape	NA	survival, knitr, lars	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
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globals	globals	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.12.5	NA	R (>= 3.1.2)	codetools	NA	NA	NA	LGPL (>= 2.1)	NA	NA	NA	NA	no	3.6.1
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gmailr	gmailr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	R (>= 3.0.0)	base64enc, crayon, gargle, httr, jsonlite, lifecycle, magrittr, mime, rematch2	NA	covr, knitr, methods, sodium, rmarkdown, testthat, xml2	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
GO.db	GO.db	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.8.2	NA	R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1)	methods, AnnotationDbi	NA	DBI	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
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gpuR	gpuR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.3	NA	R (>= 3.0.2), methods, utils	Rcpp (>= 0.12.15), assertive	Rcpp (>= 0.12.15), RcppEigen (>= 0.3.3.4.0), RViennaCL (>= 1.7.1.7), BH	testthat, knitr	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
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graphlayouts	graphlayouts	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.7.0	NA	R (>= 3.2.0)	igraph, Rcpp	Rcpp, RcppArmadillo	oaqc, testthat, ggraph, ggplot2, knitr, rmarkdown	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
gridExtra	gridExtra	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3	NA	NA	gtable, grid, grDevices, graphics, utils	NA	ggplot2, egg, lattice, knitr, testthat	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
gridGraphics	gridGraphics	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5-0	NA	grid, graphics	grDevices	NA	magick (>= 1.3), pdftools (>= 1.6)	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
gss	gss	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.2-0	NA	R (>= 3.0.0), stats	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
gsubfn	gsubfn	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.7	NA	proto	NA	NA	boot, chron, grid, lattice, quantreg, svUnit, tcltk, zoo	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
gtable	gtable	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	R (>= 3.0)	grid	NA	covr, testthat, knitr, rmarkdown, ggplot2, profvis	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
gtools	gtools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.8.2	NA	methods, stats, utils	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
gWidgets	gWidgets	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-54.2	NA	methods, utils	NA	NA	gWidgetstcltk	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
haven	haven	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.2.0	NA	R (>= 3.2)	forcats (>= 0.2.0), hms, Rcpp (>= 0.11.4), readr (>= 0.1.0), rlang (>= 0.4.0), tibble, tidyselect	Rcpp	covr, fs, knitr, rmarkdown, testthat, pillar (>= 1.4.0), cli, crayon	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.1
HDF5Array	HDF5Array	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.12.3	NA	R (>= 3.4), methods, DelayedArray (>= 0.9.3), rhdf5 (>= 2.25.6)	utils, tools, BiocGenerics (>= 0.25.1), S4Vectors, IRanges	S4Vectors (>= 0.21.6), Rhdf5lib	h5vcData, SummarizedExperiment (>= 1.9.6), GenomicRanges, ExperimentHub, TENxBrainData, BiocParallel, GenomicFeatures, BiocStyle	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
heatmaply	heatmaply	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	R (>= 3.0.0), plotly (>= 4.7.1), viridis	ggplot2 (>= 2.2.0), dendextend (>= 1.12.0), magrittr (>= 1.0.1), reshape2, scales, seriation, utils, stats, grDevices, methods, colorspace, RColorBrewer, htmlwidgets, webshot, assertthat, egg	NA	knitr, covr, gplots, tidyselect, rmarkdown, testthat	NA	GPL-2 | GPL-3	NA	NA	NA	NA	no	3.6.2
hexbin	hexbin	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.28.1	NA	R (>= 2.0.1), methods	lattice, grid, graphics, grDevices, stats, utils	NA	marray, affy, Biobase, limma, knitr	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
highlight	highlight	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.0	NA	R (>= 3.2)	grDevices, tools	NA	NA	NA	GPL (>= 3)	NA	NA	NA	NA	yes	3.6.1
highr	highr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.8	NA	R (>= 3.2.3)	NA	NA	knitr, testit	NA	GPL	NA	NA	NA	NA	no	3.6.0
hmeasure	hmeasure	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-2	NA	R (>= 2.10)	NA	NA	MASS, class, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
Hmisc	Hmisc	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	4.4-0	NA	lattice, survival (>= 3.1-6), Formula, ggplot2 (>= 2.2)	methods, latticeExtra, cluster, rpart, nnet, acepack, foreign, gtable, grid, gridExtra, data.table, htmlTable (>= 1.11.0), viridis, htmltools, base64enc	NA	chron, rms, mice, tables, knitr, ff, ffbase, plotly (>= 4.5.6), rlang	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
hms	hms	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.3	NA	NA	methods, pkgconfig, rlang, vctrs (>= 0.2.1)	NA	crayon, lubridate, pillar (>= 1.1.0), testthat	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
htmlTable	htmlTable	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.13.3	NA	NA	stringr, knitr (>= 1.6), magrittr (>= 1.5), methods, checkmate, htmlwidgets, htmltools, rstudioapi (>= 0.6)	NA	testthat, XML, xtable, ztable, Hmisc, reshape, rmarkdown, pander, chron, lubridate, tibble, tidyr (>= 0.7.2), dplyr (>= 0.7.4)	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
htmltools	htmltools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4.0	NA	R (>= 2.14.1)	utils, digest, Rcpp, rlang	Rcpp	markdown, testthat, withr	knitr	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
htmlwidgets	htmlwidgets	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5.1	NA	NA	grDevices, htmltools (>= 0.3), jsonlite (>= 0.9.16), yaml	NA	knitr (>= 1.8)	shiny (>= 1.1)	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
httpcode	httpcode	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	NA	NA	NA	testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
httpuv	httpuv	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5.2	NA	R (>= 2.15.1)	Rcpp (>= 0.11.0), utils, R6, promises, later (>= 0.8.0)	Rcpp, BH, later	testthat, callr, curl, websocket	NA	GPL (>= 2) | file LICENSE	NA	NA	NA	NA	yes	3.6.1
httr	httr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.1	NA	R (>= 3.2)	curl (>= 3.0.0), jsonlite, mime, openssl (>= 0.8), R6	NA	covr, httpuv, jpeg, knitr, png, readr, rmarkdown, testthat (>= 0.8.0), xml2	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
hunspell	hunspell	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.0	NA	R (>= 3.0.2)	Rcpp, digest	Rcpp (>= 0.12.12)	spelling, testthat, pdftools, janeaustenr, wordcloud2, knitr, stopwords, rmarkdown	NA	GPL-2 | LGPL-2.1 | MPL-1.1	NA	NA	NA	NA	yes	3.6.1
hwriter	hwriter	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.2	NA	R (>= 2.6.0)	NA	NA	NA	NA	LGPL-2.1	NA	NA	NA	NA	no	3.6.1
igraph	igraph	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.5	NA	methods	graphics, grDevices, magrittr, Matrix, pkgconfig (>= 2.0.0), stats, utils	NA	ape, digest, graph, igraphdata, rgl, scales, stats4, tcltk, testthat, withr	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
imager	imager	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.42.3	NA	R (>= 2.10.0),magrittr	Rcpp (>= 0.11.5),methods,stringr,png,jpeg,readbitmap,grDevices,purrr,downloader,igraph	Rcpp	knitr, rmarkdown,ggplot2,dplyr,scales, testthat,OpenMPController,raster,spatstat, magick,Cairo	NA	LGPL-3	NA	NA	NA	NA	yes	3.6.2
import	import	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	NA	NA	NA	knitr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
imputeMissings	imputeMissings	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0.3	NA	NA	randomForest,stats	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
inflection	inflection	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.5	NA	NA	parallel, stats, graphics, grDevices	NA	knitr, rmarkdown	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
influenceR	influenceR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.0	NA	R (>= 3.2.0)	igraph (>= 1.0.1), Matrix (>= 1.1-4), methods, utils	NA	testthat	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
ini	ini	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.1	NA	NA	NA	NA	testthat	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
inTrees	inTrees	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2	NA	NA	RRF, arules, gbm, xtable, xgboost, data.table, methods	NA	NA	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.0
inum	inum	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-1	NA	R (>= 3.3.0)	stats, libcoin (>= 1.0-0)	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
ipred	ipred	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9-9	NA	R (>= 2.10)	rpart (>= 3.1-8), MASS, survival, nnet, class, prodlim	NA	mvtnorm, mlbench, TH.data	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.0
IRanges	IRanges	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.18.3	NA	R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.21.9)	stats4	S4Vectors	XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
irlba	irlba	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3.3	NA	Matrix	stats, methods	Matrix	NA	NA	GPL-3	NA	NA	NA	NA	yes	3.6.0
isoband	isoband	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.1	NA	NA	Rcpp, grid, utils	Rcpp, testthat	covr, ggplot2, knitr, magick, microbenchmark, rmarkdown, sf, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
ISwR	ISwR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0-8	NA	R (>= 2.6.0)	NA	NA	survival,MASS	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
iterators	iterators	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.12	NA	R (>= 2.5.0), utils	NA	NA	RUnit, foreach	NA	Apache License (== 2.0)	NA	NA	NA	NA	no	3.6.1
itertools	itertools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-3	NA	R (>= 2.14.0), iterators(>= 1.0.0)	parallel	NA	foreach	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
janitor	janitor	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.1	NA	R (>= 3.1.2)	dplyr (>= 0.7.0), lifecycle, lubridate, magrittr, purrr, rlang, stringi, stringr, snakecase (>= 0.9.2), tidyselect (>= 1.0.0), tidyr (>= 0.7.0)	NA	knitr, rmarkdown, sf, testthat, tibble, tidygraph	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
jomo	jomo	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.6-10	NA	NA	stats, lme4, survival, MASS, ordinal	NA	mitml	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
jpeg	jpeg	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-8.1	NA	R (>= 2.9.0)	NA	NA	NA	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
jsonlite	jsonlite	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.1	NA	methods	NA	NA	httr, curl, plyr, testthat, knitr, rmarkdown, R.rsp, sp	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
kableExtra	kableExtra	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	R (>= 3.1.0)	knitr (>= 1.16), magrittr, stringr (>= 1.0), xml2 (>= 1.1.1), rvest, rmarkdown (>= 1.6.0), readr, scales, viridisLite, stats, grDevices, htmltools, rstudioapi, glue, tools, webshot, digest	NA	testthat, magick, formattable, dplyr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
KEGGgraph	KEGGgraph	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.44.0	NA	R (>= 2.10.0)	methods, XML (>= 2.3-0), graph, utils, RCurl	NA	Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
KEGGREST	KEGGREST	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.24.1	NA	NA	methods, httr, png, Biostrings	NA	RUnit, BiocGenerics, knitr	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
keras	keras	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.2.5.0	NA	R (>= 3.2)	generics (>= 0.0.1), reticulate (>= 1.10), tensorflow (>= 2.0.0), tfruns (>= 1.0), magrittr, zeallot, methods, R6	NA	ggplot2, testthat (>= 2.1.0), knitr, rmarkdown, tfdatasets, jpeg	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
kernlab	kernlab	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9-29	NA	R (>= 2.10)	methods, stats, grDevices, graphics	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
klaR	klaR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6-15	NA	R (>= 2.10.0), MASS	combinat, questionr, grDevices, stats, utils, graphics	NA	scatterplot3d (>= 0.3-22), som, mlbench, rpart, e1071	NA	GPL-2 | GPL-3	NA	NA	NA	NA	no	3.6.2
km.ci	km.ci	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5-2	NA	R (>= 1.8.0), survival, stats	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	NA	3.6.0
KMsurv	KMsurv	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-5	NA	NA	NA	NA	NA	NA	GPL (>= 3)	NA	NA	NA	NA	NA	3.6.0
knitcitations	knitcitations	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.10	NA	R (>= 3.0)	RefManageR (>= 0.8.2), digest, httr (>= 0.3), methods, utils	NA	testthat, knitr (>= 1.6)	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
knitr	knitr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.28	NA	R (>= 3.2.3)	evaluate (>= 0.10), highr, markdown, stringr (>= 0.6), yaml (>= 2.1.19), methods, xfun, tools	NA	formatR, testit, digest, rgl (>= 0.95.1201), codetools, rmarkdown, htmlwidgets (>= 0.7), webshot, tikzDevice (>= 0.10), tinytex, reticulate (>= 1.4), JuliaCall (>= 0.11.1), magick, png, jpeg, gifski, xml2 (>= 1.2.0), httr, DBI (>= 0.4-1), showtext, tibble, sass, styler (>= 1.2.0)	NA	GPL	NA	NA	NA	NA	no	3.6.2
ks	ks	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.11.7	NA	R (>= 2.10.0)	FNN (>= 1.1), kernlab, KernSmooth (>= 2.22), Matrix, mclust, mgcv, multicool, mvtnorm (>= 1.0-0)	NA	maps, MASS, misc3d (>= 0.4-0), OceanView, oz, rgl (>= 0.66)	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
labeling	labeling	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3	NA	NA	NA	NA	NA	NA	MIT + file LICENSE | Unlimited	NA	NA	NA	NA	no	3.6.0
labelled	labelled	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3.1	NA	NA	haven (>= 2.1.0), dplyr, stats	NA	testthat, knitr, rmarkdown, questionr, snakecase	memisc	GPL-3	NA	NA	NA	NA	no	3.6.2
laeken	laeken	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.1	NA	R (>= 3.2.0)	boot, MASS	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
Lahman	Lahman	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	7.0-1	NA	R (>= 2.10)	dplyr	NA	lattice, ggplot2, googleVis, data.table, vcd, reshape2, tidyr, zipcode, knitr, rmarkdown, car	NA	GPL	NA	NA	NA	NA	no	3.6.1
lambda.r	lambda.r	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.4	NA	R (>= 3.0.0)	formatR	NA	testit	NA	LGPL-3	NA	NA	NA	NA	no	3.6.1
LambertW	LambertW	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.4	NA	MASS, ggplot2,	lamW (>= 1.0.0), stats, graphics, grDevices, RColorBrewer, reshape2, Rcpp	Rcpp, lamW	boot, Rsolnp, nortest, numDeriv, testthat, moments,	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
lamW	lamW	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.0	NA	R (>= 3.0.2)	Rcpp, RcppParallel (>= 4.3.20)	Rcpp, RcppParallel (>= 4.3.20)	testthat	NA	BSD_2_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
lars	lars	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2	NA	R (>= 2.10)	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
later	later	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	NA	Rcpp (>= 0.12.9), rlang	Rcpp, BH	knitr, rmarkdown, testthat	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
latticeExtra	latticeExtra	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6-29	NA	R (>= 3.6.0), lattice	grid, stats, utils, grDevices, png, jpeg, RColorBrewer	NA	maps, mapproj, deldir, tripack, quantreg, zoo, MASS, mgcv	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
lava	lava	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.7	NA	R (>= 3.0)	grDevices, graphics, methods, numDeriv, stats, survival, SQUAREM, utils	NA	KernSmooth, Matrix, Rgraphviz, data.table, ellipse, fields, foreach, geepack, gof (>= 0.9), graph, igraph (>= 0.6), lava.tobit (>= 0.4.7), lme4, mets (>= 1.1), nlme, optimx, polycor, quantreg, rgl, testthat (>= 0.11), visNetwork, zoo	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
lava.tobit	lava.tobit	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5	NA	lava (>= 1.5), mets (>= 1.2.2), mvtnorm, survival	NA	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
lavaan	lavaan	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6-5	NA	R(>= 3.4)	methods, stats4, stats, utils, graphics, MASS, mnormt, pbivnorm, numDeriv	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
lazyeval	lazyeval	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.2	NA	R (>= 3.1.0)	NA	NA	knitr, rmarkdown (>= 0.2.65), testthat, covr	NA	GPL-3	NA	NA	NA	NA	yes	3.6.0
LDheatmap	LDheatmap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.99-7	NA	R (>= 2.14.0)	grid, genetics, snpStats, Rcpp	Rcpp	rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, lattice, ggplot2, vcfR	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
leaps	leaps	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.1	NA		NA	NA	biglm	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
libcoin	libcoin	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-5	NA	R (>= 3.4.0)	stats, mvtnorm	mvtnorm	coin	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
LiblineaR	LiblineaR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.10-8	NA	NA	NA	NA	SparseM	NA	GPL-2	NA	NA	NA	NA	yes	3.6.0
lifecycle	lifecycle	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.0	NA	R (>= 3.2)	glue, rlang (>= 0.4.0)	NA	covr, crayon, knitr, rmarkdown, testthat (>= 2.1.0)	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
limma	limma	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.40.6	NA	R (>= 3.6.0)	grDevices, graphics, stats, utils, methods	NA	affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn	NA	GPL (>=2)	NA	NA	NA	NA	yes	3.6.1
lintr	lintr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.1	NA	R (>= 3.2)	rex, crayon, codetools, cyclocomp, testthat (>= 2.2.1), digest, rstudioapi (>= 0.2), httr (>= 1.2.1), jsonlite, knitr, stats, utils, xml2 (>= 1.0.0), xmlparsedata (>= 1.0.3)	NA	rmarkdown, mockery	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
listenv	listenv	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.8.0	NA	R (>= 3.1.2)	NA	NA	R.utils, R.rsp, markdown	NA	LGPL (>= 2.1)	NA	NA	NA	NA	no	3.6.1
lm.beta	lm.beta	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5-1	NA	NA	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
lme4	lme4	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-23	NA	R (>= 3.2.0), Matrix (>= 1.2-1), methods, stats	graphics, grid, splines, utils, parallel, MASS, lattice, boot, nlme (>= 3.1-123), minqa (>= 1.1.15), nloptr (>= 1.0.4), statmod	Rcpp (>= 0.10.5), RcppEigen	knitr, rmarkdown, PKPDmodels, MEMSS, testthat (>= 0.8.1), ggplot2, mlmRev, optimx (>= 2013.8.6), gamm4, pbkrtest, HSAUR2, numDeriv, car, dfoptim	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
lmom	lmom	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.8	NA	R (>= 3.0.0)	stats, graphics	NA	NA	NA	Common Public License Version 1.0	NA	NA	NA	NA	yes	3.6.1
lmtest	lmtest	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9-37	NA	R (>= 3.0.0), stats, zoo	graphics	NA	car, strucchange, sandwich, dynlm, stats4, survival, AER	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
locfit	locfit	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5-9.4	NA	R (>= 3.5.0)	lattice	NA	interp, gam	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
logcondens	logcondens	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1.5	NA	R (>= 2.10)	ks, graphics, stats	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
LogicReg	LogicReg	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.2	NA	R (>= 2.10), survival	stats, graphics, utils, grDevices	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
lsr	lsr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5	NA	NA	NA	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
lubridate	lubridate	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.7.8	NA	methods, R (>= 3.2)	generics, Rcpp (>= 0.12.13)	Rcpp	covr, knitr, testthat	chron, timeDate, tis, zoo	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
magick	magick	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3	NA	NA	Rcpp (>= 0.12.12), magrittr, curl	Rcpp	av (>= 0.3), spelling, jsonlite, methods, knitr, rmarkdown, rsvg, webp, pdftools, ggplot2, raster, rgdal, gapminder, IRdisplay, tesseract (>= 2.0), gifski	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
magrittr	magrittr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5	NA	NA	NA	NA	testthat, knitr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
manipulateWidget	manipulateWidget	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.10.1	NA	NA	shiny (>= 1.0.3), miniUI, htmltools, htmlwidgets, knitr, methods, tools, base64enc, grDevices, codetools, webshot	NA	dygraphs, leaflet, plotly, xts, rmarkdown, testthat, covr	NA	GPL (>= 2) | file LICENSE	NA	NA	NA	NA	no	3.6.2
mapdata	mapdata	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3.0	NA	R (>= 2.14.0), maps (>= 2.0-7)	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
mapproj	mapproj	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.7	NA	R (>= 3.0.0), maps (>= 2.3-0)	stats, graphics	NA	NA	NA	Lucent Public License	NA	NA	NA	NA	yes	3.6.2
maps	maps	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.3.0	NA	R (>= 3.0.0)	graphics, utils	NA	mapproj (>= 1.2-0), mapdata (>= 2.3.0), sp, maptools, rnaturalearth	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
maptools	maptools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9-9	NA	R (>= 2.10), sp (>= 1.0-11)	foreign (>= 0.8), methods, grid, lattice, stats, utils, grDevices	NA	rgeos (>= 0.1-8), spatstat (>= 1.60), PBSmapping, maps, RColorBrewer, raster, polyclip, spatstat.utils	gpclib, RArcInfo	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
markdown	markdown	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1	NA	R (>= 2.11.1)	utils, xfun, mime (>= 0.3)	NA	knitr, RCurl	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
MASS	MASS	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	7.3-51.6	recommended	R (>= 3.1.0), grDevices, graphics, stats, utils	methods	NA	lattice, nlme, nnet, survival	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
Matching	Matching	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	4.9-7	NA	R (>= 2.6.0), MASS (>= 7.2-1), graphics, grDevices, stats	NA	NA	parallel, rgenoud (>= 2.12), rbounds	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
MatchIt	MatchIt	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.0.2	NA	R (>= 2.6)	MASS, Matching	NA	cem, nnet, optmatch, rpart, mgcv, WhatIf, R.rsp, testthat, rgenoud	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
matlab	matlab	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.2	NA	R (>= 2.15)	methods	NA	NA	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
MatrixModels	MatrixModels	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-1	NA	R (>= 3.0.1)	stats, methods, Matrix (>= 1.1-5)	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.0
matrixStats	matrixStats	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.56.0	NA	R (>= 2.12.0)	NA	NA	base64enc, ggplot2, knitr, microbenchmark, R.devices, R.rsp	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.2
maxstat	maxstat	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.7-25	NA	R (>= 1.7.0)	exactRankTests(>= 0.8-23), mvtnorm(>= 0.5-10), stats, graphics	NA	TH.data, survival	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.0
mboost	mboost	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.9-2	NA	R (>= 3.2.0), methods, stats, parallel, stabs (>= 0.5-0)	Matrix, survival, splines, lattice, nnls, quadprog, utils, graphics, grDevices, partykit (>= 1.2-1)	NA	TH.data, MASS, fields, BayesX, gbm, mlbench, RColorBrewer, rpart (>= 4.0-3), randomForest, nnet, testthat (>= 0.10.0), kangar00	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
mclust	mclust	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	5.4.6	NA	R (>= 3.0)	stats, utils, graphics, grDevices	NA	knitr (>= 1.12), rmarkdown (>= 0.9), mix (>= 1.0), geometry (>= 0.3-6), MASS	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
mda	mda	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5	NA	R (>= 3.5.0), stats, class	NA	NA	earth, testthat	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
memisc	memisc	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.99.22	NA	R (>= 3.3.0), lattice, stats, methods, utils, MASS	grid, repr, data.table	NA	splines, knitr, rmarkdown, sandwich	AER, car, eha, lme4, ordinal, simex, tibble, haven	GPL-2	NA	NA	NA	NA	yes	3.6.2
memoise	memoise	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	NA	digest (>= 0.6.3)	NA	testthat, aws.s3, httr, covr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
mets	mets	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.7.1	NA	R (>= 3.5), timereg (>= 1.9.4), lava (>= 1.6.6)	mvtnorm, numDeriv, compiler, Rcpp, splines, survival (>= 2.43-1),	Rcpp, RcppArmadillo, mvtnorm	prodlim, testthat (>= 0.11), ucminf, R.rsp (>= 0.40)	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
mgcv	mgcv	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.8-31	recommended	R (>= 2.14.0), nlme (>= 3.1-64)	methods, stats, graphics, Matrix, splines, utils	NA	parallel, survival, MASS	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
mice	mice	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.8.0	NA	R (>= 2.10.0)	broom, dplyr, graphics, lattice, methods, stats, tidyr, utils	Rcpp	knitr, lme4, MASS, mitml, miceadds, nnet, pan, randomForest, rmarkdown, rpart, survival, testthat	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
microbenchmark	microbenchmark	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4-7	NA	NA	graphics, stats	NA	ggplot2, multcomp, RUnit	NA	BSD_2_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.1
mime	mime	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9	NA	NA	tools	NA	NA	NA	GPL	NA	NA	NA	NA	yes	3.6.2
miniUI	miniUI	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.1.1	NA	NA	shiny (>= 0.13), htmltools (>= 0.3), utils	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
minqa	minqa	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.4	NA	NA	Rcpp (>= 0.9.10)	Rcpp	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.0
OmicSelector	OmicSelector	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.0	NA	NA	dplyr, remotes, devtools, BiocManager, plyr, epiDisplay, rsq, MASS, caret, pROC, ggplot2, DMwR, ROSE, gridExtra, gplots, stringr, data.table, doParallel, Boruta, spFSR, varSelRF, My.stepwise, psych, C50, randomForest, nnet, reticulate, stargazer, ggrepel, classInt, plotly, keras, cutpointr, naniar, visdat, imputeMissings, foreach, deepnet, snow, calibrate, networkD3, VennDiagram, RSNNS, kernlab, car, PairedData, profileR, xgboost, kableExtra	NA	knitr, rmarkdown,	NA	License: MIT + file LICENSE	NA	NA	NA	NA	NA	3.6.2
miRNAtap	miRNAtap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.18.0	NA	R (>= 3.3.0), AnnotationDbi	DBI, RSQLite, stringr, sqldf, plyr, methods	NA	topGO, org.Hs.eg.db, miRNAtap.db, testthat	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
miRNAtap.db	miRNAtap.db	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.99.10	NA	miRNAtap	AnnotationDbi, DBI, RSQLite, miRNAtap	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
missForest	missForest	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4	NA	randomForest,foreach,itertools	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.0
mitml	mitml	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3-7	NA	NA	pan, jomo, haven, grDevices, graphics, stats, utils	NA	mice, miceadds, Amelia, lme4, nlme, geepack, survival, knitr, rmarkdown	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.0
mixOmics	mixOmics	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	6.8.5	NA	R (>= 3.5.0), MASS, lattice, ggplot2	igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, utils	NA	BiocStyle, knitr, rmarkdown, testthat, rgl	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
mlbench	mlbench	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1-1	NA	R (>= 2.10)	NA	NA	lattice	NA	GPL-2	NA	NA	NA	NA	NA	3.6.1
MLmetrics	MLmetrics	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.1	NA	R (>= 2.10)	stats, utils, ROCR	NA	e1071	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
mlr	mlr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.17.1	NA	ParamHelpers (>= 1.10), R (>= 3.0.2)	backports (>= 1.1.0), BBmisc (>= 1.11), checkmate (>= 1.8.2), data.table (>= 1.12.4), ggplot2, methods, parallelMap (>= 1.3), stats, stringi, survival, utils, XML	NA	ada, adabag, bartMachine, batchtools, brnn, bst, C50, care, caret (>= 6.0-57), class, clue, cluster, ClusterR, clusterSim (>= 0.44-5), cmaes, cowplot, CoxBoost, crs, Cubist, deepnet, DiceKriging, DiscriMiner, e1071, earth, elasticnet, emoa, evtree, extraTrees, fda.usc, FDboost, FNN, forecast (>= 8.3), fpc, frbs, FSelector, FSelectorRcpp (>= 0.2.1), gbm, GenSA, ggpubr, glmnet, GPfit, h2o (>= 3.6.0.8), Hmisc, hrbrthemes, irace (>= 2.0), kernlab, kknn, klaR, knitr, laGP, LiblineaR, lintr (>= 1.0.0.9001), MASS, mboost, mco, mda, memoise, mlbench, mldr, mlrMBO, mmpf, modeltools, mRMRe, neuralnet, nnet, nodeHarvest (>= 0.7-3), numDeriv, pamr, pander, party, penalized (>= 0.9-47), pls, PMCMR (>= 4.1), praznik (>= 5.0.0), randomForest, randomForestSRC (>= 2.7.0), ranger (>= 0.8.0), rappdirs, refund, rex, rFerns, rgenoud, rknn, rmarkdown, ROCR, rotationForest, rpart, RRF, rrlda, rsm, RSNNS, rucrdtw, RWeka, sda, sf, smoof, sparseLDA, stepPlr, survAUC, svglite, SwarmSVM, testthat, tgp, TH.data, tidyr, tsfeatures, vdiffr, wavelets, xgboost (>= 0.7)	NA	BSD_2_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
mnormt	mnormt	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5-7	NA	R (>= 2.2.0)	NA	NA	NA	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
mockery	mockery	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4.2	NA	NA	testthat	NA	knitr, rmarkdown (>= 1.0), R6	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
mockr	mockr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1	NA	NA	lazyeval	NA	testthat, covr	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
ModelMetrics	ModelMetrics	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.2.2	NA	R (>= 3.2.2)	Rcpp, data.table	Rcpp	testthat	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
modelr	modelr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.7	NA	R (>= 3.2)	broom, dplyr, magrittr, purrr (>= 0.2.2), rlang (>= 0.2.0), tibble, tidyr (>= 0.8.0), tidyselect	NA	compiler, covr, ggplot2, testthat	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
modeltools	modeltools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2-23	NA	stats, stats4	methods	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
moments	moments	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.14	NA	NA	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
mRMRe	mRMRe	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1.0	NA	survival, igraph, methods	NA	NA	NA	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
mstate	mstate	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.12	NA	survival (>= 3.1)	RColorBrewer	NA	cmprsk	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
multcomp	multcomp	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4-13	NA	stats, graphics, mvtnorm (>= 1.0-10), survival (>= 2.39-4), TH.data (>= 1.0-2)	sandwich (>= 2.3-0), codetools	NA	lme4 (>= 0.999375-16), nlme, robustbase, coin, MASS, foreign, xtable, lmtest, coxme (>= 2.2-1), SimComp, ISwR, tram (>= 0.2-5)	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
multicool	multicool	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-11	NA	methods, Rcpp (>= 0.11.2)	NA	Rcpp	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
munsell	munsell	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.0	NA	NA	colorspace, methods	NA	ggplot2, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
mvtnorm	mvtnorm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-0	NA	R(>= 3.5.0)	stats, methods	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
mxnet	mxnet	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5.0	NA	R (>= 3.4.4)	methods, Rcpp (>= 0.12.1), DiagrammeR (>= 0.9.0), visNetwork (>= 1.0.3), data.table, jsonlite, magrittr, stringr	Rcpp	testthat, mlbench, knitr, rmarkdown, imager, covr	NA	Apache License (== 2.0)	NA	NA	NA	NA	NA	3.6.1
My.stepwise	My.stepwise	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.0	NA	R (>= 3.3.3)	car, lmtest, survival, stats	NA	NA	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.2
naniar	naniar	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.1	NA	R (>= 3.1.2)	dplyr, ggplot2, purrr, tidyr, tibble (>= 2.0.0), magrittr, stats, visdat, rlang, forcats, viridis, glue, UpSetR	NA	knitr, rmarkdown, testthat (>= 2.1.0), rpart, rpart.plot, covr, gridExtra, wakefield, vdiffr, here, simputation, imputeTS, gdtools, Hmisc, spelling	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
networkD3	networkD3	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4	NA	R (>= 3.0.0)	htmlwidgets (>= 0.3.2), igraph, magrittr	NA	htmltools (>= 0.2.6), jsonlite,	knitr, shiny	GPL (>= 3)	NA	NA	NA	NA	no	3.6.2
neuralnet	neuralnet	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.44.2	NA	R (>= 2.9.0)	grid, MASS, grDevices, stats, utils, Deriv	NA	testthat	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
nloptr	nloptr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.2.1	NA	NA	NA	NA	testthat (>= 0.8.1), knitr, rmarkdown, inline (>= 0.3.14)	NA	LGPL-3	NA	NA	NA	NA	yes	3.6.2
NLP	NLP	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2-0	NA	R (>= 3.2.0)	utils	NA	NA	udpipe, spacyr, cleanNLP	GPL-3	NA	NA	NA	NA	no	3.6.1
nnls	nnls	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4	NA	NA	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	NA	3.6.0
NOISeq	NOISeq	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.28.0	NA	R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2)	NA	NA	NA	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
nor1mix	nor1mix	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3-0	NA	NA	stats, graphics	NA	cluster	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
nortest	nortest	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-4	NA	NA	stats	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
np	np	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.60-10	NA	NA	boot, cubature, methods, quadprog, quantreg, stats	NA	MASS	NA	GPL	NA	NA	NA	NA	yes	3.6.2
numDeriv	numDeriv	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2016.8-1.1	NA	R (>= 2.11.1)	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
nycflights13	nycflights13	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.1	NA	R (>= 3.2)	tibble	NA	dplyr	NA	CC0	NA	NA	NA	NA	no	3.6.1
olsrr	olsrr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.3	NA	R(>= 3.3)	car, data.table, ggplot2, goftest, graphics, gridExtra, nortest, Rcpp, stats, utils	Rcpp	covr, descriptr, knitr, rmarkdown, testthat, vdiffr, xplorerr	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
openintro	openintro	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.7.1	NA	graphics, grDevices, stats, utils, R (>= 2.10)	NA	NA	NA	NA	GPL-2 | GPL-3	NA	NA	NA	NA	no	3.6.0
openssl	openssl	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.1	NA	NA	askpass	NA	testthat, digest, knitr, rmarkdown, jsonlite, jose, sodium	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.1
openxlsx	openxlsx	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	4.1.5	NA	R (>= 3.3.0)	grDevices, methods, Rcpp, stats, utils, zip, stringi	Rcpp	knitr, testthat, roxygen2	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
optimx	optimx	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2020-4.2	NA	NA	numDeriv	NA	knitr, rmarkdown, setRNG, BB, ucminf, minqa, dfoptim, lbfgsb3c, lbfgs, subplex	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
ordinal	ordinal	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2019.12-10	NA	R (>= 2.13.0), stats, methods	ucminf, MASS, Matrix, numDeriv	NA	lme4, nnet, xtable, testthat (>= 0.8), tools	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
ordinalNet	ordinalNet	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.7	NA	NA	stats, graphics	NA	testthat (>= 1.0.2), MASS (>= 7.3-45), glmnet (>= 2.0-5), penalized (>= 0.9-50), glmnetcr (>= 1.0.3), VGAM (>= 1.0-3), rms (>= 5.1-0)	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.1
org.Hs.eg.db	org.Hs.eg.db	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.8.2	NA	R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1)	methods, AnnotationDbi	NA	DBI, annotate, RUnit	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
oro.dicom	oro.dicom	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.3	NA	R (>= 2.14.0)	utils, oro.nifti (>= 0.4.0)	NA	testthat, hwriter	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	no	3.6.1
oro.nifti	oro.nifti	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.10.1	NA	R (>= 2.14.0)	stats, bitops, splines, graphics, grDevices, methods, utils, abind, RNifti (>= 0.9.0)	NA	XML, testthat, covr, knitr, rmarkdown	dcemriS4, fmri, oro.dicom	BSD_3_clause + file LICENSE	NA	NA	NA	NA	no	3.6.2
pacman	pacman	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.1	NA	R (>= 3.5.0)	remotes, methods, stats, utils	NA	BiocManager, knitr, lattice, testthat (>= 0.9.0), XML	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
PairedData	PairedData	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.1	NA	methods,graphics,MASS,gld,mvtnorm,lattice,ggplot2	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
pamr	pamr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.56.1	NA	R (>= 2.10), cluster, survival	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
pan	pan	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6	NA	NA	NA	NA	mitools, lme4	NA	GPL-3	NA	no	NA	NA	yes	3.6.0
pander	pander	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.3	NA	R (>= 2.15.0)	grDevices, graphics, methods, utils, stats, digest, tools, Rcpp	Rcpp	grid, lattice, ggplot2 (>= 0.9.2), sylly, sylly.en, futile.logger, survival, microbenchmark, zoo, nlme, descr, MASS, knitr, rmarkdown, tables, reshape, memisc, Epi, randomForest, tseries, gtable, rms, forecast, data.table	NA	AGPL-3 | file LICENSE	NA	NA	NA	NA	yes	3.6.1
parallelMap	parallelMap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5.0	NA	R (>= 3.0.0)	BBmisc (>= 1.8), checkmate (>= 1.8.0), parallel, stats, utils	NA	BatchJobs (>= 1.8), batchtools (>= 0.9.6), data.table, Rmpi, rpart, snow, testthat	NA	BSD_2_clause + file LICENSE	NA	NA	NA	NA	no	3.6.2
ParamHelpers	ParamHelpers	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.14	NA	NA	backports, BBmisc (>= 1.10), checkmate (>= 1.8.2), fastmatch, methods	NA	akima, covr, eaf, emoa, GGally, ggplot2, grid, gridExtra, irace (>= 2.1), lhs, plyr, reshape2, testthat	NA	BSD_2_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
parsedate	parsedate	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.0	NA	NA	rematch2	NA	covr, testthat, withr	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
party	party	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3-4	NA	R (>= 3.0.0), methods, grid, stats, mvtnorm (>= 1.0-2), modeltools (>= 0.2-21), strucchange	survival (>= 2.37-7), coin (>= 1.1-0), zoo, sandwich (>= 1.1-1)	mvtnorm	TH.data (>= 1.0-3), mlbench, colorspace, MASS, vcd, ipred, varImp	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
partykit	partykit	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2-7	NA	R (>= 3.1.0), graphics, grid, libcoin (>= 1.0-0), mvtnorm	grDevices, stats, utils, survival, Formula (>= 1.2-1), inum (>= 1.0-0), rpart (>= 4.1-11)	NA	XML, pmml, rJava, sandwich, strucchange, vcd, AER, mlbench, TH.data (>= 1.0-3), coin (>= 1.1-0), RWeka (>= 0.4-19), datasets, parallel, psychotools (>= 0.3-0), psychotree, party (>= 1.3-0)	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
pastecs	pastecs	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.21	NA	NA	boot, stats, graphics, utils, grDevices	NA	svUnit, covr	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
PASWR	PASWR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1	NA	e1071, MASS, lattice	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	NA	3.6.1
pathview	pathview	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.24.0	NA	R (>= 2.10), org.Hs.eg.db	KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils	NA	gage, org.Mm.eg.db, RUnit, BiocGenerics	NA	GPL (>=3.0)	NA	NA	NA	NA	no	3.6.1
pbapply	pbapply	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4-2	NA	R (>= 3.2.0)	parallel	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
pbivnorm	pbivnorm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.0	NA	NA	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
pbkrtest	pbkrtest	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-8.6	NA	R (>= 3.6.0), lme4 (>= 1.1.10)	Matrix (>= 1.2.3), parallel, magrittr, MASS, methods	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
pca3d	pca3d	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.10.1	NA	R (>= 2.10)	rgl,ellipse	NA	knitr	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
pec	pec	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2019.11.03	NA	R (>= 2.9.0), prodlim (>= 1.4.9)	foreach (>= 1.4.2), rms (>= 4.2-0), survival (>= 2.37-7), timereg (>= 1.8.9)	NA	randomForestSRC, party, cmprsk (>= 2.2-7), rpart, CoxBoost, crrstep, riskRegression (>= 1.0.8), lava (>= 1.4.1), Hmisc (>= 3.14-4)	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
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pheatmap	pheatmap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.12	NA	R (>= 2.0)	grid, RColorBrewer, scales, gtable, stats, grDevices, graphics	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
pillar	pillar	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.4	NA	NA	cli, crayon (>= 1.3.4), fansi, rlang (>= 0.3.0), utf8 (>= 1.1.0), vctrs (>= 0.2.0)	NA	knitr, lubridate, testthat (>= 2.0.0), withr	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
pingr	pingr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.0	NA	NA	processx, utils	NA	covr, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.1
pinp	pinp	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0.9	NA	NA	rmarkdown, knitr	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
pixmap	pixmap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-11	NA	methods	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	NA	3.6.2
pkgbuild	pkgbuild	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.8	NA	R (>= 3.1)	callr (>= 3.2.0), cli, crayon, desc, prettyunits, R6, rprojroot, withr (>= 2.1.2)	NA	Rcpp, testthat, covr	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
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pkgdown	pkgdown	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5.1	NA	R (>= 3.1.0)	callr (>= 2.0.2), cli, crayon, desc, digest, evaluate, fs (>= 1.3.0), fansi, highlight, httr, magrittr, MASS, memoise, openssl, purrr, processx, rematch2, rlang (>= 0.3.0), rmarkdown (>= 1.1.9007), rstudioapi, tibble, tools, whisker, withr, xml2 (>= 1.3.1), yaml	NA	covr, htmlwidgets, jsonlite, knitr, leaflet, pkgload (>= 1.0.2), testthat (>= 2.1.0), rticles, rsconnect	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
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plogr	plogr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.0	NA	NA	NA	NA	Rcpp	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
plotly	plotly	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	4.9.2.1	NA	R (>= 3.2.0), ggplot2 (>= 3.0.0)	tools, scales, httr, jsonlite (>= 1.6), magrittr, digest, viridisLite, base64enc, htmltools (>= 0.3.6), htmlwidgets (>= 1.3), tidyr, hexbin, RColorBrewer, dplyr, tibble, lazyeval (>= 0.2.0), rlang, crosstalk, purrr, data.table, promises	NA	MASS, maps, ggthemes, GGally, testthat, knitr, devtools, shiny (>= 1.1.0), shinytest (>= 1.3.0), curl, rmarkdown, vdiffr, Cairo, broom, webshot, listviewer, dendextend, sf, maptools, rgeos, png, IRdisplay, processx, plotlyGeoAssets, forcats	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
plotmo	plotmo	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.5.7	NA	R (>= 3.4.0), Formula (>= 1.2-3), plotrix, TeachingDemos	NA	NA	C50 (>= 0.1.0-24), earth (>= 5.1.0), gbm (>= 2.1.1), glmnet (>= 2.0.5), glmnetUtils (>= 1.0.3), MASS (>= 7.3-45), mlr (>= 2.12.1), neuralnet (>= 1.33), partykit (>= 1.2-2), pre (>= 0.5.0), rpart (>= 4.1-10), rpart.plot (>= 2.1.0)	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
plotrix	plotrix	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.7-8	NA	R (>= 3.5.0)	grDevices, graphics, stats, utils	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
pls	pls	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.7-2	NA	R (>= 2.10)	grDevices, graphics, methods, stats	NA	MASS, parallel, Rmpi, testthat, RUnit	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
plyr	plyr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.8.6	NA	R (>= 3.1.0)	Rcpp (>= 0.11.0)	Rcpp	abind, covr, doParallel, foreach, iterators, itertools, tcltk, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
pmml	pmml	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.3.1	NA	XML	methods, stats, utils, stringr	NA	ada, amap, arules, caret, clue, data.table, forecast, gbm, glmnet, Matrix, neighbr, nnet, rpart, randomForestSRC (<= 2.5.0), randomForest, rattle, kernlab, e1071, testthat, survival, xgboost, knitr, rmarkdown, covr	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	no	3.6.2
png	png	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-7	NA	R (>= 2.9.0)	NA	NA	NA	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
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praise	praise	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	NA	NA	NA	testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
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preprocessCore	preprocessCore	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.46.0	NA	NA	stats	NA	NA	NA	LGPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
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pROC	pROC	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.16.2	NA	R (>= 2.14)	methods, plyr, Rcpp (>= 0.11.1)	Rcpp	microbenchmark, tcltk, MASS, logcondens, doParallel, testthat, vdiffr, ggplot2	NA	GPL (>= 3)	NA	NA	NA	NA	yes	3.6.2
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proto	proto	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	NA	NA	NA	testthat, covr	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
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ps	ps	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.3	NA	R (>= 3.1)	utils	NA	callr, covr, curl, pingr, processx (>= 3.1.0), R6, rlang, testthat, tibble	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
pspearman	pspearman	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3-0	NA	NA	NA	NA	NA	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
psych	psych	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.9.12.31	NA	NA	mnormt,parallel,stats,graphics,grDevices,methods,lattice,nlme	NA	psychTools, GPArotation, lavaan, sem, lme4,Rcsdp, graph, Rgraphviz	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
purrr	purrr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.4	NA	R (>= 3.2)	magrittr (>= 1.5), rlang (>= 0.3.1)	NA	covr, crayon, dplyr (>= 0.7.8), knitr, rmarkdown, testthat, tibble, tidyselect	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	yes	3.6.2
pvclust	pvclust	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.2-0	NA	R (>= 2.10.0)	NA	NA	MASS, parallel	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
qap	qap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-1	NA	NA	NA	NA	testthat	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
qtl	qtl	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.46-2	NA	R (>= 2.14.0)	parallel, graphics, stats, utils, grDevices	NA	testthat	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
quadprog	quadprog	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5-8	NA	R (>= 3.1.0)	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
quantmod	quantmod	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4.17	NA	R (>= 3.2.0), xts(>= 0.9-0), zoo, TTR(>= 0.2), methods	curl	NA	DBI,RMySQL,RSQLite,timeSeries,XML,downloader,jsonlite(>= 1.1)	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
quantreg	quantreg	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	5.55	NA	R (>= 2.6), stats, SparseM	methods, graphics, Matrix, MatrixModels	NA	tripack, akima, MASS, survival, rgl, logspline, nor1mix, Formula, zoo, R.rsp	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
questionr	questionr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.7.0	NA	R (>= 2.10)	shiny (>= 1.0.5), miniUI, rstudioapi, highr, classInt, htmltools, graphics, stats, utils, labelled (>= 2.0.0)	NA	memisc, testthat, roxygen2, dplyr, tidyr, janitor, forcats, knitr	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.0
qvalue	qvalue	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.16.0	NA	R(>= 2.10)	splines, ggplot2, grid, reshape2	NA	knitr	NA	LGPL	NA	NA	NA	NA	no	3.6.1
qvcalc	qvcalc	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.2	NA	NA	NA	NA	relimp, MASS	psychotools, survival	GPL-2 | GPL-3	NA	NA	NA	NA	no	3.6.2
R.methodsS3	R.methodsS3	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.8.0	NA	R (>= 2.13.0)	utils	NA	codetools	NA	LGPL (>= 2.1)	NA	NA	NA	NA	no	3.6.2
R.oo	R.oo	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.23.0	NA	R (>= 2.13.0), R.methodsS3 (>= 1.7.1)	methods, utils	NA	tools	NA	LGPL (>= 2.1)	NA	NA	NA	NA	no	3.6.1
R.utils	R.utils	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.9.2	NA	R (>= 2.14.0), R.oo (>= 1.23.0)	methods, utils, tools, R.methodsS3 (>= 1.7.1)	NA	digest (>= 0.6.10)	NA	LGPL (>= 2.1)	NA	NA	NA	NA	no	3.6.2
R6	R6	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.4.1	NA	R (>= 3.0)	NA	NA	knitr, microbenchmark, pryr, testthat, ggplot2, scales	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
randomForest	randomForest	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	4.6-14	NA	R (>= 3.2.2), stats	NA	NA	RColorBrewer, MASS	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
ranger	ranger	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.12.1	NA	R (>= 3.1)	Rcpp (>= 0.11.2), Matrix	Rcpp, RcppEigen	survival, testthat	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
RANN	RANN	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.6.1	NA	NA	NA	NA	testthat	NA	GPL (>= 3)	NA	NA	NA	NA	yes	3.6.1
rappdirs	rappdirs	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.1	NA	R (>= 2.14), methods	NA	NA	testthat, roxygen2	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.1
rARPACK	rARPACK	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.11-0	NA	NA	RSpectra	NA	Matrix (>= 1.1-0)	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	no	3.6.1
raster	raster	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.1-5	NA	sp (>= 1.2-0), R (>= 3.0.0)	Rcpp, methods	Rcpp	rgdal (>= 0.9-1), rgeos (>= 0.3-8), ncdf4, igraph, tcltk, parallel, rasterVis, MASS, sf, testthat	NA	GPL (>= 3)	NA	NA	NA	NA	yes	3.6.2
rattle	rattle	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	5.3.0	NA	R (>= 3.5.0)	stats, utils, ggplot2, grDevices, graphics, magrittr, methods, stringi, stringr, tidyr, dplyr, XML, rpart.plot	NA	pmml (>= 1.2.13), bitops, colorspace, ada, amap, arules, arulesViz, biclust, cairoDevice, cba, cluster, corrplot, descr, doBy, e1071, ellipse, fBasics, foreign, fpc, gdata, ggdendro, ggraptR, gplots, grid, gridExtra, gtools, gWidgetsRGtk2, hmeasure, Hmisc, kernlab, Matrix, mice, nnet, party, plyr, psych, randomForest, RColorBrewer, readxl, reshape, rggobi, RGtk2, ROCR, RODBC, rpart, scales, SnowballC, survival, timeDate, tm, verification, wskm, xgboost	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
rattle.data	rattle.data	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.2	NA	R (>= 2.10)	NA	NA	rattle	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
rcmdcheck	rcmdcheck	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.3	NA	NA	callr (>= 3.1.1.9000), cli (>= 1.1.0), crayon, desc (>= 1.2.0), digest, pkgbuild, prettyunits, R6, rprojroot, sessioninfo (>= 1.1.1), utils, withr, xopen	NA	covr, knitr, mockery, rmarkdown, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
RColorBrewer	RColorBrewer	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-2	NA	R (>= 2.0.0)	NA	NA	NA	NA	Apache License 2.0	NA	NA	NA	NA	no	3.6.0
Rcpp	Rcpp	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.4.6	NA	NA	methods, utils	NA	tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2)	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
RcppAnnoy	RcppAnnoy	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0.16	NA	R (>= 3.1)	methods, Rcpp (>= 0.11.3)	Rcpp	tinytest	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
RcppArmadillo	RcppArmadillo	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9.870.2.0	NA	R (>= 3.3.0)	Rcpp (>= 0.11.0), stats, utils, methods	Rcpp	tinytest, Matrix, pkgKitten, reticulate, slam	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
RcppCNPy	RcppCNPy	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.10	NA	R (>= 3.1.0)	methods, Rcpp	Rcpp	knitr, rmarkdown, pinp, reticulate	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
RcppEigen	RcppEigen	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.3.7.0	NA	R (>= 2.15.1)	Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils	Rcpp	inline, tinytest, pkgKitten, microbenchmark	NA	GPL (>= 2) | file LICENSE	NA	NA	NA	NA	yes	3.6.1
RcppHNSW	RcppHNSW	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.0	NA	NA	methods, Rcpp (>= 0.11.3)	Rcpp	testthat, covr	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
RcppNumerical	RcppNumerical	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-0	NA	NA	Rcpp	Rcpp, RcppEigen	knitr, rmarkdown, prettydoc, mvtnorm, RcppEigen	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
RcppParallel	RcppParallel	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	5.0.1	NA	R (>= 3.0.2)	NA	NA	Rcpp, RUnit, knitr, rmarkdown	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
RcppRoll	RcppRoll	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	R (>= 2.15.1)	Rcpp	Rcpp	zoo, testthat	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.0
RCurl	RCurl	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.98-1.2	NA	R (>= 3.4.0), methods	bitops	NA	XML	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
readbitmap	readbitmap	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.5	NA	NA	bmp, jpeg, png, tiff	NA	pixmap, testthat	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
readr	readr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.1	NA	R (>= 3.1)	Rcpp (>= 0.12.0.5), tibble, hms (>= 0.4.1), R6, clipr, crayon, methods	Rcpp, BH	curl, testthat, knitr, rmarkdown, stringi, covr, spelling	NA	GPL (>= 2) | file LICENSE	NA	NA	NA	NA	yes	3.6.1
readxl	readxl	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.1	NA	NA	cellranger, Rcpp (>= 0.12.18), tibble (>= 1.3.1), utils	progress, Rcpp	covr, knitr, rmarkdown, rprojroot (>= 1.1), testthat	NA	GPL-3	NA	NA	NA	NA	yes	3.6.0
rebus	rebus	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-3	NA	R (>= 3.1.0)	rebus.base (>= 0.0-3), rebus.datetimes, rebus.numbers, rebus.unicode (>= 0.0-2)	NA	testthat	NA	Unlimited	NA	NA	NA	NA	no	3.6.1
rebus.base	rebus.base	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-3	NA	R (>= 3.1.0)	stats	NA	stringi, testthat	NA	Unlimited	NA	NA	NA	NA	no	3.6.1
rebus.datetimes	rebus.datetimes	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-1	NA	R (>= 3.1.0)	rebus.base	NA	stats, testthat	NA	Unlimited	NA	NA	NA	NA	no	3.6.1
rebus.numbers	rebus.numbers	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-1	NA	R (>= 3.1.0)	rebus.base, utils	NA	testthat	NA	Unlimited	NA	NA	NA	NA	no	3.6.1
rebus.unicode	rebus.unicode	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-2	NA	R (>= 3.1.0)	rebus.base (>= 0.0-2)	NA	stringi	NA	Unlimited	NA	NA	NA	NA	no	3.6.1
recipes	recipes	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.12	NA	R (>= 3.1), dplyr	generics, glue, gower, ipred, lubridate, magrittr, Matrix, purrr (>= 0.2.3), rlang (>= 0.4.0), stats, tibble, tidyr (>= 0.8.3), tidyselect (>= 0.2.5), timeDate, utils, withr	NA	covr, ddalpha, dimRed (>= 0.2.2), fastICA, ggplot2, igraph, kernlab, knitr, modeldata, pls, RANN, RcppRoll, rmarkdown, rpart, rsample, RSpectra, testthat (>= 2.1.0), xml2	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
RefManageR	RefManageR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.12	NA	R (>= 3.0)	xml2, jsonlite, utils, plyr, tools, httr, bibtex (>= 0.4.1), lubridate (>= 1.5.0), stringr, methods	NA	knitr, testthat,	NA	GPL-2 | GPL-3 | BSD_3_clause + file LICENSE	NA	NA	NA	NA	no	3.6.1
reghelper	reghelper	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.6	NA	R (>= 3.1.0)	ggplot2 (>= 1.0.0), stats, nlme, lme4, utils	NA	testthat (>= 0.8.1)	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
registry	registry	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5-1	NA	R (>= 2.6.0)	utils	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
regress	regress	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3-15	NA	NA	NA	NA	nlme, MASS	NA	GPL	NA	NA	NA	NA	no	3.6.1
rematch	rematch	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.1	NA	NA	NA	NA	covr, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
rematch2	rematch2	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1.2	NA	NA	tibble	NA	covr, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
remote	remote	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.1	NA	R (>= 2.10), Rcpp (>= 0.10.3), raster, methods	grDevices, gridExtra, latticeExtra, mapdata, scales, stats, utils	Rcpp	maps, lattice, grid, sp	NA	GPL (>= 3) | file LICENSE	NA	NA	NA	NA	yes	3.6.2
remotes	remotes	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1.1	NA	R (>= 3.0.0)	methods, stats, tools, utils	NA	brew, callr, codetools, curl, covr, git2r (>= 0.23.0), knitr, mockery, pkgbuild (>= 1.0.1), pingr, rmarkdown, rprojroot, testthat, withr	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
repr	repr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	R (>= 3.0.1)	utils, grDevices, htmltools, jsonlite, pillar (>= 1.4.0), base64enc	NA	methods, highr, Cairo, stringr, testthat, diffobj (>= 0.2.3), leaflet	data.table, dplyr, htmlwidgets, vegalite, plotly, geojsonio	GPL-3	NA	NA	NA	NA	no	3.6.2
reprex	reprex	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	R (>= 3.1)	callr (>= 2.0.0), clipr (>= 0.4.0), fs, rlang, rmarkdown, utils, whisker, withr	NA	covr, devtools, fortunes, knitr, miniUI, rprojroot, rstudioapi, shiny, styler (>= 1.0.2), testthat (>= 2.0.0)	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
repurrrsive	repurrrsive	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	R (>= 2.10)	tibble, utils	NA	gapminder, jsonlite, purrr, rprojroot, testthat (>= 2.1.0), wesanderson, xml2	NA	CC0	NA	NA	NA	NA	no	3.6.1
reshape	reshape	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.8.8	NA	R (>= 2.6.1)	plyr	NA	NA	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.0
reshape2	reshape2	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.4	NA	R (>= 3.1)	plyr (>= 1.8.1), Rcpp, stringr	Rcpp	covr, lattice, testthat (>= 0.8.0)	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
reticulate	reticulate	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.15	NA	R (>= 3.0)	graphics, jsonlite, Matrix, methods, rappdirs, Rcpp (>= 0.12.7), utils	Rcpp	callr, knitr, rmarkdown, testthat	NA	Apache License 2.0	NA	NA	NA	NA	yes	3.6.2
rex	rex	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.0	NA	NA	lazyeval	NA	testthat, knitr, rmarkdown, dplyr, ggplot2, magrittr, Hmisc, stringr, rvest, roxygen2, covr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
rgeos	rgeos	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5-3	NA	R (>= 3.3.0), methods, sp (>= 1.1-0)	utils, stats, graphics	sp	maptools (>= 0.8-5), testthat, XML, maps, rgdal	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
rgexf	rgexf	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.16.0	NA	NA	XML, igraph, grDevices, utils, servr	NA	knitr, rmarkdown, testthat, covr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
rgl	rgl	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.100.54	NA	R (>= 3.2.0)	graphics, grDevices, stats, utils, htmlwidgets, htmltools, knitr, jsonlite (>= 0.9.20), shiny, magrittr, crosstalk, manipulateWidget (>= 0.9.0)	NA	MASS, rmarkdown, deldir, orientlib, lattice, misc3d, rstudioapi, magick, plotrix (>= 3.7-3), tripack, interp, alphashape3d, tcltk	NA	GPL	NA	NA	NA	NA	yes	3.6.2
Rgraphviz	Rgraphviz	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.28.0	NA	R (>= 2.6.0), methods, utils, graph, grid	stats4, graphics, grDevices	NA	RUnit, BiocGenerics, XML	NA	EPL	NA	NA	NA	NA	yes	3.6.1
rhdf5	rhdf5	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.28.1	NA	R (>= 3.5.0), methods	Rhdf5lib (>= 1.3.2)	Rhdf5lib	bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark, dplyr, ggplot2	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
Rhdf5lib	Rhdf5lib	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.3	NA	NA	NA	NA	BiocStyle, knitr, rmarkdown	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
Rhtslib	Rhtslib	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.16.3	NA	NA	zlibbioc	zlibbioc	BiocStyle, knitr	NA	LGPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
rhub	rhub	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.1	NA	NA	assertthat, callr, cli (>= 1.1.0), crayon, desc, digest, httr, jsonlite, parsedate, pillar, prettyunits, processx, R6, rappdirs, rcmdcheck (>= 1.2.1), rematch, tibble, utils, uuid, whoami, withr	NA	covr, testthat, knitr, rmarkdown	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
rio	rio	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.16	NA	R (>= 2.15.0)	tools, stats, utils, foreign, haven (>= 1.1.0), curl (>= 0.6), data.table (>= 1.9.8), readxl (>= 0.1.1), openxlsx, tibble	NA	datasets, bit64, testthat, knitr, magrittr, clipr, csvy, feather, fst, hexView, jsonlite, readODS (>= 1.6.4), readr, rmatio, xml2 (>= 1.2.0), yaml	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
RISmed	RISmed	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1.7	NA	R (>= 2.8.0), methods	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.0
rJava	rJava	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9-12	NA	R (>= 2.5.0), methods	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
rjson	rjson	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2.20	NA	R (>= 3.1.0)	NA	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
rlang	rlang	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4.6	NA	R (>= 3.2.0)	NA	NA	cli, covr, crayon, glue, magrittr, methods, pillar, rmarkdown, testthat (>= 2.3.0), vctrs (>= 0.2.3)	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
rmarkdown	rmarkdown	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1	NA	R (>= 3.0)	tools, utils, knitr (>= 1.22), yaml (>= 2.1.19), htmltools (>= 0.3.5), evaluate (>= 0.13), base64enc, jsonlite, mime, tinytex (>= 0.11), xfun, methods, stringr (>= 1.2.0)	NA	shiny (>= 0.11), tufte, testthat, digest, dygraphs, tibble, fs, pkgdown, callr (>= 2.0.0)	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
rmdformats	rmdformats	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.7	NA	NA	knitr, rmarkdown, bookdown, htmltools	NA	questionr	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
rmeta	rmeta	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.0	NA	NA	grid, stats, graphics	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
rms	rms	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	5.1-4	NA	R (>= 3.5.0), Hmisc (>= 4.3-0), survival (>= 3.1-6), lattice, ggplot2 (>= 2.2), SparseM	methods, quantreg, rpart, nlme (>= 3.1-123), polspline, multcomp, htmlTable (>= 1.11.0), htmltools	NA	boot, tcltk, plotly (>= 4.5.6)	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
RMySQL	RMySQL	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.10.20	NA	R (>= 2.8.0), DBI (>= 0.4)	methods	NA	RMariaDB, testthat, curl	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
rngtools	rngtools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5	NA	R (>= 3.2.0), methods	digest, utils, stats, parallel	NA	covr, RUnit, testthat	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
RNifti	RNifti	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.0	NA	NA	Rcpp (>= 0.11.0)	Rcpp	testthat (>= 0.11.0), covr, reportr, shades	oro.nifti, tractor.base	GPL-2	NA	NA	NA	NA	yes	3.6.2
robustbase	robustbase	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.93-6	NA	R (>= 3.1.0)	stats, graphics, utils, methods, DEoptimR	NA	grid, MASS, lattice, boot, cluster, Matrix, robust, fit.models, MPV, xtable, ggplot2, GGally, RColorBrewer, reshape2, sfsmisc, catdata, doParallel, foreach, skewt	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
ROCR	ROCR	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-11	NA	R (>= 3.6)	methods, graphics, grDevices, gplots, stats	NA	testthat, knitr, rmarkdown	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
RODBC	RODBC	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3-16	NA	R (>= 3.0.0)	stats	NA	NA	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
Rook	Rook	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-1	NA	R (>= 2.13.0)	utils, tools, methods, brew	NA	NA	NA	GPL-2	NA	NA	NA	NA	yes	3.6.1
ROSE	ROSE	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.0-3	NA	NA	NA	NA	MASS, nnet, rpart, tree	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
rowr	rowr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.3	NA	R (>= 3.0.1)	methods	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
roxygen2	roxygen2	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	7.1.0	NA	R (>= 3.2)	brew, commonmark, desc (>= 1.2.0), digest, knitr, methods, pkgload (>= 1.0.2), purrr (>= 0.3.3), R6 (>= 2.1.2), Rcpp (>= 0.11.0), rlang, stringi, stringr (>= 1.0.0), utils, xml2	Rcpp	covr, devtools, rmarkdown, testthat (>= 2.1.0), R.methodsS3, R.oo	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
roxygen2md	roxygen2md	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	NA	desc, devtools, enc, rex, rlang, tibble, usethis, withr	NA	rstudioapi, testthat	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
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rpart.plot	rpart.plot	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.0.8	NA	R (>= 3.4.0), rpart (>= 4.1-10)	NA	NA	earth (>= 5.1.0)	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
rpartScore	rpartScore	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-1	NA	R (>= 2.14.2), rpart	NA	NA	MASS	NA	GPL (>= 2)	NA	NA	NA	NA	NA	3.6.0
RPostgreSQL	RPostgreSQL	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6-2	NA	R (>= 2.9.0), methods, DBI (>= 0.3)	NA	NA	NA	NA	GPL-2 | file LICENSE	NA	NA	NA	NA	yes	3.6.1
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RRF	RRF	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.9.1	NA	R (>= 2.5.0), stats	NA	NA	RColorBrewer, MASS	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.0
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RSNNS	RSNNS	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-12	NA	R (>= 2.10.0), methods, Rcpp (>= 0.8.5)	NA	Rcpp	scatterplot3d,NeuralNetTools	NA	LGPL (>= 2) | file LICENSE	NA	NA	NA	NA	yes	3.6.2
rsnps	rsnps	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	NA	plyr, stringr, crul (>= 0.5.2), data.table, XML, xml2, jsonlite	NA	testthat, knitr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
RSpectra	RSpectra	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.16-0	NA	R (>= 3.0.2)	Matrix (>= 1.1-0), Rcpp (>= 0.11.5)	Rcpp, RcppEigen (>= 0.3.3.3.0)	knitr, rmarkdown, prettydoc	NA	MPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
rsq	rsq	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0	NA	NA	methods, stats, MASS, lme4, nlme, numDeriv, Matrix	NA		NA	GPL-2	NA	NA	NA	NA	no	3.6.2
RSQLite	RSQLite	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.2.0	NA	R (>= 3.1.0)	bit64, blob (>= 1.2.0), DBI (>= 1.1.0), memoise, methods, pkgconfig, Rcpp (>= 0.12.7)	BH, plogr (>= 0.2.0), Rcpp	DBItest (>= 1.7.0), knitr, rmarkdown, testthat	NA	LGPL (>= 2.1)	NA	NA	NA	NA	yes	3.6.1
rstatix	rstatix	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.0	NA	R (>= 3.3.0)	stats, utils, tidyr (>= 1.0.0), purrr, broom, rlang (>= 0.3.1), tibble (>= 2.1.3), dplyr (>= 0.7.1), magrittr, corrplot, tidyselect (>= 1.0.0), car	NA	knitr, rmarkdown, ggpubr, graphics, emmeans, coin, boot, testthat, spelling	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
rstudioapi	rstudioapi	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.11	NA	NA	NA	NA	testthat, knitr, rmarkdown, clipr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
Rsubread	Rsubread	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.34.7	NA	NA	grDevices, stats, utils	NA	NA	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
rsvd	rsvd	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.3	NA	R (>= 3.2.2)	Matrix	NA	ggplot2, testthat	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.2
rtracklayer	rtracklayer	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.44.4	NA	R (>= 3.3), methods, GenomicRanges (>= 1.31.8)	XML (>= 1.98-0), BiocGenerics (>= 0.25.1), S4Vectors (>= 0.19.22), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), tools	S4Vectors, IRanges, XVector	BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit	NA	Artistic-2.0 + file LICENSE	NA	NA	NA	NA	yes	3.6.1
RVAideMemoire	RVAideMemoire	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9-75	NA	NA	ade4 (>= 1.7-8), boot, car, FactoMineR, graphics, grDevices, lme4 (>= 1.0-4), MASS, mixOmics, nnet, pls, pspearman, stats, utils, vegan (>= 2.4-3)	NA	dgof, emmeans, ordinal, survival	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
rvcheck	rvcheck	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.8	NA	R (>= 3.4.0)	BiocManager, utils, rlang	NA	NA	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.2
rversions	rversions	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.1	NA	NA	curl, utils, xml2 (>= 1.0.0)	NA	mockery, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
rvest	rvest	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.5	NA	R (>= 3.2), xml2	httr (>= 0.5), magrittr, selectr	NA	covr, knitr, png, rmarkdown, spelling, stringi (>= 0.3.1), testthat	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
RViennaCL	RViennaCL	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.7.1.8	NA	NA	NA	NA	gpuR	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
RWeka	RWeka	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-42	NA	R (>= 2.6.0)	RWekajars (>= 3.9.3-1), rJava (>= 0.6-3), graphics, stats, utils, grid	NA	partykit (>= 0.8.0), mlbench, e1071	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
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sandwich	sandwich	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.5-1	NA	R (>= 2.10.0)	stats, utils, zoo	NA	AER, car, geepack, lattice, lmtest, MASS, multiwayvcov, parallel, pcse, plm, pscl, scatterplot3d, stats4, strucchange, survival	NA	GPL-2 | GPL-3	NA	NA	NA	NA	no	3.6.0
scales	scales	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.1	NA	R (>= 3.2)	farver (>= 2.0.3), labeling, lifecycle, munsell (>= 0.5), R6, RColorBrewer, viridisLite	NA	bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), testthat (>= 2.1.0)	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
scater	scater	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.12.2	NA	R (>= 3.6), SingleCellExperiment, ggplot2	BiocGenerics, SummarizedExperiment, Matrix, dplyr, ggbeeswarm, grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel	Rcpp, beachmat	BiocStyle, biomaRt, beachmat, cowplot, destiny, knitr, mvoutlier, rmarkdown, Rtsne, uwot, testthat, magrittr, pheatmap, Biobase, limma	NA	GPL-3	NA	NA	NA	NA	yes	3.6.0
scatterplot3d	scatterplot3d	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3-41	NA	R (>= 2.7.0)	grDevices, graphics, stats	NA	NA	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
segmented	segmented	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-0	NA	NA	NA	NA	NA	NA	GPL	NA	NA	NA	NA	no	3.6.1
selectr	selectr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-2	NA	R (>= 3.0)	methods, stringr, R6	NA	testthat, XML, xml2	NA	BSD_3_clause + file LICENCE	NA	NA	NA	NA	no	3.6.1
seqinr	seqinr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.6-1	NA	R (>= 2.10.0)	ade4,segmented	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
seriation	seriation	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2-8	NA	R (>= 2.14.0)	TSP, qap, grid, cluster, gclus, dendextend, colorspace, MASS, gplots, registry, methods, stats, grDevices	NA	biclust, testthat, DendSer, GA	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
servr	servr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.16	NA	R (>= 3.0.0)	mime (>= 0.2), httpuv (>= 1.4.0), xfun, jsonlite	NA	tools, later, rstudioapi, knitr (>= 1.9), rmarkdown	NA	GPL	NA	NA	NA	NA	no	3.6.2
sessioninfo	sessioninfo	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.1	NA	NA	cli, tools, utils, withr	NA	callr, covr, mockery, testthat	NA	GPL-2	NA	NA	NA	NA	no	3.6.0
sf	sf	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.9-3	NA	methods, R (>= 3.3.0)	classInt (>= 0.4-1), DBI (>= 0.8), graphics, grDevices, grid, magrittr, Rcpp (>= 0.12.18), stats, tools, units (>= 0.6-0), utils	Rcpp	blob, covr, dplyr (>= 0.8-3), ggplot2, knitr, lwgeom (>= 0.2-1), maps, mapview, microbenchmark, odbc, pillar, pool, raster, rgdal, rgeos, rlang, rmarkdown, RPostgres (>= 1.1.0), RPostgreSQL, RSQLite, sp (>= 1.2-4), spatstat, spatstat.utils, stars (>= 0.2-0), testthat, tibble (>= 1.4.1), tidyr (>= 1.0-0), tmap (>= 2.0), vctrs	NA	GPL-2 | MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
shape	shape	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.4	NA	R (>= 2.01)	stats, graphics, grDevices	NA	NA	NA	GPL (>= 3)	NA	NA	NA	NA	no	3.6.1
shiny	shiny	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.0.2	NA	R (>= 3.0.2), methods	utils, grDevices, httpuv (>= 1.5.2), mime (>= 0.3), jsonlite (>= 0.9.16), xtable, digest, htmltools (>= 0.4.0), R6 (>= 2.0), sourcetools, later (>= 1.0.0), promises (>= 1.1.0), tools, crayon, rlang (>= 0.4.0), fastmap (>= 1.0.0)	NA	datasets, Cairo (>= 1.5-5), testthat (>= 2.1.1), knitr (>= 1.6), markdown, rmarkdown, ggplot2, reactlog (>= 1.0.0), magrittr, yaml	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	no	3.6.2
shinythemes	shinythemes	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1.2	NA	R (>= 3.0.0)	shiny (>= 0.11)	NA	NA	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	no	3.6.1
ShortRead	ShortRead	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.42.0	NA	BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)	Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra,	S4Vectors, IRanges, XVector, Biostrings	BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
SingleCellExperiment	SingleCellExperiment	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.0	NA	SummarizedExperiment	S4Vectors, methods, BiocGenerics, utils, stats	NA	testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne, Matrix	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
slam	slam	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-47	NA	R (>= 3.4.0)	stats	NA	NA	Matrix, SparseM, spam	GPL-2	NA	NA	NA	NA	yes	3.6.1
snakecase	snakecase	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.11.0	NA	R (>= 3.2)	stringr, stringi	NA	testthat, covr, tibble, purrrlyr, knitr, rmarkdown, magrittr	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
snow	snow	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4-3	NA	R (>= 2.13.1), utils	NA	NA	Rmpi,rlecuyer,nws	NA	GPL	NA	NA	NA	NA	no	3.6.2
SnowballC	SnowballC	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.7.0	NA	NA	NA	NA	NA	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
snpStats	snpStats	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.34.0	NA	R(>= 2.10.0), survival, Matrix, methods	graphics, grDevices, stats, utils, BiocGenerics, zlibbioc	NA	hexbin	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
sourcetools	sourcetools	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.7	NA	R (>= 3.0.2)	NA	NA	testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.0
sp	sp	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4-1	NA	R (>= 3.0.0), methods	utils, stats, graphics, grDevices, lattice, grid	NA	RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat, maptools, deldir	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
spam	spam	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.5-1	NA	R (>= 3.1), dotCall64, grid, methods	NA	NA	spam64, fields, SparseM, Matrix, testthat, R.rsp, truncdist, knitr, rmarkdown	NA	LGPL-2 | BSD_3_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.1
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spelling	spelling	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.1	NA	NA	commonmark, xml2, hunspell (>= 3.0), knitr	NA	pdftools	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
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strucchange	strucchange	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.5-2	NA	R (>= 2.10.0), zoo, sandwich	graphics, stats, utils	NA	stats4, car, dynlm, e1071, foreach, lmtest, mvtnorm, tseries	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
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survival	survival	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.1-12	recommended	R (>= 3.4.0)	graphics, Matrix, methods, splines, stats, utils	NA	NA	NA	LGPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
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sva	sva	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.32.1	NA	R (>= 3.2), mgcv, genefilter, BiocParallel	matrixStats, stats, graphics, utils, limma,	NA	pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
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swirl	swirl	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.4.5	NA	R (>= 3.1.0)	stringr, testthat (>= 1.0.2), httr (>= 1.1.0), yaml, RCurl, digest, tools, methods	NA	stringi	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
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tibble	tibble	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.0.1	NA	R (>= 3.1.0)	cli, crayon (>= 1.3.4), ellipsis (>= 0.2.0), fansi (>= 0.4.0), lifecycle (>= 0.2.0), magrittr, methods, pillar (>= 1.4.3), pkgconfig, rlang (>= 0.4.3), utils, vctrs (>= 0.2.4)	NA	bench, bit64, blob, covr, dplyr, evaluate, hms, htmltools, import, knitr, mockr, nycflights13, purrr, rmarkdown, testthat (>= 2.1.0), tidyr, withr	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
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tidygraph	tidygraph	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.2.0	NA	NA	tibble, dplyr (>= 0.8.5), igraph, magrittr, utils, rlang, R6, Rcpp, tools, stats, tidyr, pillar	Rcpp	network, data.tree, ape, graph, methods, testthat, covr, seriation, netrankr, influenceR, NetSwan	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.2
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tidyverse	tidyverse	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.0	NA	R (>= 3.2)	broom (>= 0.5.2), cli (>= 1.1.0), crayon (>= 1.3.4), dbplyr (>= 1.4.2), dplyr (>= 0.8.3), forcats (>= 0.4.0), ggplot2 (>= 3.2.1), haven (>= 2.2.0), hms (>= 0.5.2), httr (>= 1.4.1), jsonlite (>= 1.6), lubridate (>= 1.7.4), magrittr (>= 1.5), modelr (>= 0.1.5), pillar (>= 1.4.2), purrr (>= 0.3.3), readr (>= 1.3.1), readxl (>= 1.3.1), reprex (>= 0.3.0), rlang (>= 0.4.1), rstudioapi (>= 0.10), rvest (>= 0.3.5), stringr (>= 1.4.0), tibble (>= 2.1.3), tidyr (>= 1.0.0), xml2 (>= 1.2.2)	NA	covr, feather, glue, knitr, rmarkdown, testthat	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	no	3.6.2
tiff	tiff	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1-5	NA	R (>= 2.9.0)	NA	NA	NA	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
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timereg	timereg	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.9.4	NA	R (>= 2.15), survival	lava, numDeriv, stats, graphics, grDevices, utils, methods	NA	mets,	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
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tinytex	tinytex	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.22	NA	NA	xfun (>= 0.5)	NA	testit, rstudioapi	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
tm	tm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.7-7	NA	R (>= 3.2.0), NLP (>= 0.2-0)	Rcpp, parallel, slam (>= 0.1-37), stats, tools, utils, graphics, xml2	BH, Rcpp	antiword, filehash, methods, pdftools, Rcampdf, Rgraphviz, Rpoppler, SnowballC, testthat, tm.lexicon.GeneralInquirer	NA	GPL-3	NA	NA	NA	NA	yes	3.6.1
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truncnorm	truncnorm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0-8	NA	R (>= 3.4.0)	NA	NA	testthat	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
TSP	TSP	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.1-10	NA	R (>= 3.5.0)	graphics, foreach, utils, stats, grDevices	NA	sp, maps, maptools, testthat	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
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tweenr	tweenr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.1	NA	R (>= 3.2.0)	Rcpp (>= 0.12.3), grDevices, farver, magrittr, rlang	Rcpp	testthat, covr	NA	MIT + file LICENSE	NA	NA	NA	NA	yes	3.6.1
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varSelRF	varSelRF	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.7-8	NA	R (>= 2.0.0), randomForest, parallel	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
vcd	vcd	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4-7	NA	R (>= 2.4.0), grid	stats, utils, MASS, grDevices, colorspace, lmtest	NA	KernSmooth, mvtnorm, kernlab, HSAUR, coin	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
vctrs	vctrs	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	R (>= 3.2)	ellipsis (>= 0.2.0), digest, glue, rlang (>= 0.4.5)	NA	bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr, pillar (>= 1.4.4), pkgdown, rmarkdown, testthat (>= 2.3.0), tibble, withr, xml2, zeallot	NA	GPL-3	NA	NA	NA	NA	yes	3.6.2
vdiffr	vdiffr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.1	NA	R (>= 3.2.0)	devtools, diffobj, fontquiver (>= 0.2.0), freetypeharfbuzz (>= 0.2.5), gdtools, glue, grDevices, htmlwidgets (>= 0.6), htmltools, purrr (>= 0.2.0), rlang, R6, Rcpp, shiny, testthat (>= 1.0.0), usethis (>= 1.4.0), xml2 (>= 1.0.0)	freetypeharfbuzz, gdtools, Rcpp, BH	crayon, ggplot2 (>= 3.2.0), roxygen2, rstudioapi, withr, yaml	NA	GPL-3 | file LICENSE	NA	NA	NA	NA	yes	3.6.1
vegan	vegan	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.5-6	NA	permute (>= 0.9-0), lattice, R (>= 3.4.0)	MASS, cluster, mgcv	NA	parallel, tcltk, knitr	NA	GPL-2	NA	NA	NA	NA	yes	3.6.2
VennDiagram	VennDiagram	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.6.20	NA	R (>= 2.14.1), grid (>= 2.14.1), futile.logger	NA	NA	testthat	NA	GPL-2	NA	NA	NA	NA	no	3.6.2
verification	verification	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.42	NA	R (>= 2.10), methods, fields, boot, CircStats, MASS, dtw	graphics, stats	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.1
VIM	VIM	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	6.0.0	NA	R (>= 3.5.0),colorspace,grid	car, grDevices, magrittr, robustbase, stats, sp, vcd,MASS,nnet,e1071,methods,Rcpp,utils,graphics,laeken,ranger, data.table(>= 1.9.4)	Rcpp	dplyr, testthat (>= 2.1.0), knitr, rmarkdown	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
vipor	vipor	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4.5	NA	R (>= 3.0.0)	stats, graphics	NA	testthat, beeswarm, lattice, ggplot2, beanplot, vioplot, ggbeeswarm,	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.0
viridis	viridis	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.1	NA	R (>= 2.10), viridisLite (>= 0.3.0)	stats, ggplot2 (>= 1.0.1), gridExtra	NA	hexbin (>= 1.27.0), scales, MASS, knitr, dichromat, colorspace, rasterVis, httr, mapproj, vdiffr, svglite (>= 1.2.0), testthat, covr, rmarkdown, rgdal	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
viridisLite	viridisLite	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.3.0	NA	R (>= 2.10)	NA	NA	hexbin (>= 1.27.0), ggplot2 (>= 1.0.1), testthat, covr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
visdat	visdat	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.3	NA	R (>= 3.2.2)	ggplot2, tidyr, dplyr, purrr, readr, magrittr, stats, tibble, glue	NA	testthat, plotly (>= 4.5.6), knitr, rmarkdown, vdiffr, gdtools, spelling	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
visNetwork	visNetwork	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.9	NA	R (>= 3.0)	htmlwidgets, htmltools, jsonlite, magrittr, utils, methods, grDevices, stats	NA	knitr, rmarkdown, webshot, igraph, rpart, shiny, shinyWidgets, colourpicker, sparkline, ggraph, tidygraph, flashClust	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
vsn	vsn	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.52.0	NA	R (>= 3.4.0), Biobase	methods, affy, limma, lattice, ggplot2	NA	affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.1
webshot	webshot	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.5.2	NA	R (>= 3.0)	magrittr, jsonlite, callr	NA	httpuv, knitr, rmarkdown, shiny	NA	GPL-2	NA	NA	NA	NA	no	3.6.1
weights	weights	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.1	NA	Hmisc, gdata, mice	NA	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
whisker	whisker	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.4	NA	NA	NA	NA	markdown	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
whoami	whoami	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.0	NA	NA	httr, jsonlite, utils	NA	covr, mockery, testthat, withr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
withr	withr	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.2.0	NA	R (>= 3.2.0)	graphics, grDevices, stats	NA	covr, DBI, knitr, lattice, methods, rmarkdown, RSQLite, testthat (>= 2.1.0)	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.2
wskm	wskm	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.4.40	NA	R (>= 2.10), grDevices, stats, lattice, latticeExtra, fpc	NA	NA	NA	NA	GPL (>= 3)	NA	NA	NA	NA	yes	3.6.2
xfun	xfun	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.13	NA	NA	stats, tools	NA	testit, parallel, rstudioapi, tinytex, mime, markdown, knitr, htmltools, base64enc, remotes, rmarkdown	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.2
xgboost	xgboost	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0.2	NA	R (>= 3.3.0)	Matrix (>= 1.1-0), methods, data.table (>= 1.9.6), magrittr (>= 1.5), stringi (>= 0.5.2)	NA	knitr, rmarkdown, ggplot2 (>= 1.0.1), DiagrammeR (>= 0.9.0), Ckmeans.1d.dp (>= 3.3.1), vcd (>= 1.3), testthat, lintr, igraph (>= 1.0.1), jsonlite, float	NA	Apache License (== 2.0) | file LICENSE	NA	NA	NA	NA	yes	3.6.2
XLConnect	XLConnect	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.1	NA	R (>= 2.10.0)	methods, rJava	NA	RUnit, lattice, ggplot2 (>= 0.9.3), zoo	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
XLConnectJars	XLConnectJars	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.2-15	NA	NA	rJava	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.1
xlsx	xlsx	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.3	NA	NA	rJava, xlsxjars, grDevices, utils	NA	rprojroot, testthat, covr, tibble, knitr, rmarkdown, RefManageR	NA	GPL-3	NA	NA	NA	NA	no	3.6.2
xlsxjars	xlsxjars	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.6.1	NA	rJava	NA	NA	NA	NA	GPL-3	NA	NA	NA	NA	no	3.6.0
XML	XML	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	3.99-0.3	NA	R (>= 2.13.0), methods, utils	NA	NA	bitops, RCurl	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
xml2	xml2	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.3.2	NA	R (>= 3.1.0)	methods	NA	covr, curl, httr, knitr, magrittr, mockery, rmarkdown, testthat (>= 2.1.0)	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
xmlparsedata	xmlparsedata	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.3	NA	R (>= 3.0.0)	NA	NA	covr, testthat, xml2	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.1
xopen	xopen	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.0.0	NA	R (>= 3.1)	processx	NA	ps, testthat	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
xtable	xtable	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.8-4	NA	R (>= 2.10.0)	stats, utils	NA	knitr, plm, zoo, survival	NA	GPL (>= 2)	NA	NA	NA	NA	no	3.6.0
xts	xts	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.12-0	NA	zoo (>= 1.7-12)	methods	zoo	timeSeries, timeDate, tseries, chron, fts, tis, RUnit	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
XVector	XVector	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.24.0	NA	R (>= 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= 0.21.13), IRanges (>= 2.15.12)	methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges	S4Vectors, IRanges	Biostrings, drosophila2probe, RUnit	NA	Artistic-2.0	NA	NA	NA	NA	yes	3.6.0
yaml	yaml	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.2.1	NA	NA	NA	NA	RUnit	NA	BSD_3_clause + file LICENSE	NA	NA	NA	NA	yes	3.6.2
zeallot	zeallot	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	0.1.0	NA	NA	NA	NA	testthat, knitr, rmarkdown, purrr, magrittr	NA	MIT + file LICENSE	NA	NA	NA	NA	no	3.6.0
zip	zip	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	2.0.4	NA	NA	NA	NA	covr, processx, R6, testthat, withr	NA	CC0	NA	NA	NA	NA	yes	3.6.1
zlibbioc	zlibbioc	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.30.0	NA	NA	NA	NA	NA	NA	Artistic-2.0 + file LICENSE	NA	NA	NA	NA	yes	3.6.0
zoo	zoo	/home/konrad/R/x86_64-pc-linux-gnu-library/3.6	1.8-8	NA	R (>= 3.1.0), stats	utils, graphics, grDevices, lattice (>= 0.20-27)	NA	AER, coda, chron, fts, ggplot2 (>= 3.0.0), mondate, scales, strucchange, timeDate, timeSeries, tis, tseries, xts	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
BiocManager.1	BiocManager	/usr/local/lib/R/site-library	1.30.4	NA	R (>= 3.5.0)	utils	NA	BiocStyle, BiocVersion, remotes, testthat, knitr, withr	NA	Artistic-2.0	NA	NA	NA	NA	no	3.6.1
survival.1	survival	/usr/local/lib/R/site-library	2.44-1.1	recommended	R (>= 2.13.0)	graphics, Matrix, methods, splines, stats, utils	NA	NA	NA	LGPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
base	base	/usr/lib/R/library	3.6.2	base	NA	NA	NA	methods	NA	Part of R 3.6.2	NA	NA	NA	NA	NA	3.6.2
boot	boot	/usr/lib/R/library	1.3-25	recommended	R (>= 3.0.0), graphics, stats	NA	NA	MASS, survival	NA	Unlimited	NA	NA	NA	NA	no	3.6.2
class	class	/usr/lib/R/library	7.3-17	recommended	R (>= 3.0.0), stats, utils	MASS	NA	NA	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
cluster.1	cluster	/usr/lib/R/library	2.1.0	recommended	R (>= 3.3.0)	graphics, grDevices, stats, utils	NA	MASS, Matrix	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
codetools	codetools	/usr/lib/R/library	0.2-16	recommended	R (>= 2.1)	NA	NA	NA	NA	GPL	NA	NA	NA	NA	no	3.6.0
compiler	compiler	/usr/lib/R/library	3.6.2	base	NA	NA	NA	NA	NA	Part of R 3.6.2	NA	NA	NA	NA	NA	3.6.2
datasets	datasets	/usr/lib/R/library	3.6.2	base	NA	NA	NA	NA	NA	Part of R 3.6.2	NA	NA	NA	NA	NA	3.6.2
foreign	foreign	/usr/lib/R/library	0.8-76	recommended	R (>= 3.0.0)	methods, utils, stats	NA	NA	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
graphics	graphics	/usr/lib/R/library	3.6.2	base	NA	grDevices	NA	NA	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
grDevices	grDevices	/usr/lib/R/library	3.6.2	base	NA	NA	NA	KernSmooth	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
grid	grid	/usr/lib/R/library	3.6.2	base	NA	grDevices, utils	NA	lattice	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
KernSmooth	KernSmooth	/usr/lib/R/library	2.23-17	recommended	R (>= 2.5.0), stats	NA	NA	MASS	NA	Unlimited	NA	NA	NA	NA	yes	3.6.2
lattice	lattice	/usr/lib/R/library	0.20-41	recommended	R (>= 3.0.0)	grid, grDevices, graphics, stats, utils	NA	KernSmooth, MASS, latticeExtra	chron	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
MASS.1	MASS	/usr/lib/R/library	7.3-51.5	recommended	R (>= 3.1.0), grDevices, graphics, stats, utils	methods	NA	lattice, nlme, nnet, survival	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
Matrix	Matrix	/usr/lib/R/library	1.2-18	recommended	R (>= 3.2.0)	methods, graphics, grid, stats, utils, lattice	NA	expm, MASS	MatrixModels, graph, SparseM, sfsmisc	GPL (>= 2) | file LICENCE	NA	NA	NA	NA	yes	3.6.1
methods	methods	/usr/lib/R/library	3.6.2	base	NA	utils, stats	NA	codetools	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
mgcv.1	mgcv	/usr/lib/R/library	1.8-31	recommended	R (>= 2.14.0), nlme (>= 3.1-64)	methods, stats, graphics, Matrix, splines, utils	NA	parallel, survival, MASS	NA	GPL (>= 2)	NA	NA	NA	NA	yes	3.6.1
nlme	nlme	/usr/lib/R/library	3.1-147	recommended	R (>= 3.4.0)	graphics, stats, utils, lattice	NA	Hmisc, MASS	NA	GPL (>= 2) | file LICENCE	NA	NA	NA	NA	yes	3.6.2
nnet	nnet	/usr/lib/R/library	7.3-14	recommended	R (>= 3.0.0), stats, utils	NA	NA	MASS	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
parallel	parallel	/usr/lib/R/library	3.6.2	base	NA	tools, compiler	NA	methods	snow, nws, Rmpi	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
rpart.1	rpart	/usr/lib/R/library	4.1-15	recommended	R (>= 2.15.0), graphics, stats, grDevices	NA	NA	survival	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.1
spatial	spatial	/usr/lib/R/library	7.3-12	recommended	R (>= 3.0.0), graphics, stats, utils	NA	NA	MASS	NA	GPL-2 | GPL-3	NA	NA	NA	NA	yes	3.6.2
splines	splines	/usr/lib/R/library	3.6.2	base	NA	graphics, stats	NA	Matrix, methods	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
stats	stats	/usr/lib/R/library	3.6.2	base	NA	utils, grDevices, graphics	NA	MASS, Matrix, SuppDists, methods, stats4	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
stats4	stats4	/usr/lib/R/library	3.6.2	base	NA	graphics, methods, stats	NA	NA	NA	Part of R 3.6.2	NA	NA	NA	NA	NA	3.6.2
survival.2	survival	/usr/lib/R/library	3.1-8	recommended	R (>= 3.4.0)	graphics, Matrix, methods, splines, stats, utils	NA	NA	NA	LGPL (>= 2)	NA	NA	NA	NA	yes	3.6.2
tcltk	tcltk	/usr/lib/R/library	3.6.2	base	NA	utils	NA	NA	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
tools	tools	/usr/lib/R/library	3.6.2	base	NA	NA	NA	codetools, methods, xml2, curl, commonmark	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2
utils	utils	/usr/lib/R/library	3.6.2	base	NA	NA	NA	methods, xml2, commonmark	NA	Part of R 3.6.2	NA	NA	NA	NA	yes	3.6.2